Method for rapidly screening microbial hosts to identify certain strains with improved yield and/or quality in the expression of heterologous proteins

ABSTRACT

The present invention provides an array for rapidly identifying a host cell population capable of producing a heterologous protein with improved yield and/or quality. The array comprises one or more host cell populations that have been genetically modified to increase the expression of one or more target genes involved in protein production, decrease the expression of one or more target genes involved in protein degradation, or both. One or more of the strains in the array may express the heterologous protein of interest in a periplasm compartment or may secrete the heterologous protein extracellularly through an outer cell wall. The strain arrays are useful for screening for improved expression of any protein of interest including therapeutic proteins, hormones, growth factors, extracellular receptors or ligands, proteases, kinases, blood proteins, chemokines, cytokines, antibodies and the like.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation-in-Part of U.S. application Ser. No. 12/109,554, filed Apr. 25, 2008, incorporated by reference herein, which claims the benefit of U.S. Provisional Application No. 60/914,361, filed Apr. 27, 2007, incorporated by reference herein.

REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB

The official copy of the sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 38194701.txt, a creation date of Oct. 30, 2009 and a size of 352 KB. The sequence listing filed via EFS-Web is part of the specification and is herein incorporated by reference in its entirety.

FIELD OF THE INVENTION

This invention relates to the field of protein production, particularly to identifying optimal host cells for large-scale production of properly processed heterologous proteins.

BACKGROUND OF THE INVENTION

More than 150 recombinantly produced proteins and polypeptides have been approved by the U.S. Food and Drug Administration (FDA) for use as biotechnology drugs and vaccines, with another 370 in clinical trials. Unlike small molecule therapeutics that are produced through chemical synthesis, proteins and polypeptides are most efficiently produced in living cells. However, current methods of production of recombinant proteins in bacteria often produce improperly folded, aggregated or inactive proteins, and many types of proteins require secondary modifications that are inefficiently achieved using known methods.

Numerous attempts have been developed to increase production of properly folded proteins in recombinant systems. For example, investigators have changed fermentation conditions (Schein (1989) Bio/Technology, 7:1141-1149), varied promoter strength, or used overexpressed chaperone proteins (Hockney (1994) Trends Biotechnol. 12:456-463), which can help prevent the formation of inclusion bodies.

Strategies have been developed to excrete proteins from the cell into the supernatant. For example, U.S. Pat. No. 5,348,867; U.S. Pat. No. 6,329,172; PCT Publication No. WO 96/17943; PCT Publication No. WO 02/40696; and U.S. Application Publication 2003/0013150. Other strategies for increased expression are directed to targeting the protein to the periplasm. Some investigations focus on non-Sec type secretion (see for e.g. PCT Publication No. WO 03/079007; U.S. Publication No. 2003/0180937; U.S. Publication No. 2003/0064435; and, PCT Publication No. WO 00/59537). However, the majority of research has focused on the secretion of exogenous proteins with a Sec-type secretion system.

A number of secretion signals have been described for use in expressing recombinant polypeptides or proteins. See, for example, U.S. Pat. No. 5,914,254; U.S. Pat. No. 4,963,495; European Patent No. 0 177 343; U.S. Pat. No. 5,082,783; PCT Publication No. WO 89/10971; U.S. Pat. No. 6,156,552; U.S. Pat. Nos. 6,495,357; 6,509,181; 6,524,827; 6,528,298; 6,558,939; 6,608,018; 6,617,143; U.S. Pat. Nos. 5,595,898; 5,698,435; and 6,204,023; U.S. Pat. No. 6,258,560; PCT Publication Nos. WO 01/21662, WO 02/068660 and U.S. Application Publication 2003/0044906; U.S. Pat. No. 5,641,671; and European Patent No. EP 0 121 352.

Heterologous protein production often leads to the formation of insoluble or improperly folded proteins, which are difficult to recover and may be inactive. Furthermore, the presence of specific host cell proteases may degrade the protein of interest and thus reduce the final yield. There is no single factor that will improve the production of all heterologous proteins. As a result, there is a need in the art for identifying improved large-scale expression systems capable of secreting and properly processing recombinant polypeptides to produce transgenic proteins in properly processed form.

SUMMARY OF THE INVENTION

The present invention provides compositions and methods for rapidly identifying a host cell population capable of producing at least one heterologous polypeptide according to a desired specification with improved yield and/or quality. The compositions comprise two or more host cell populations that have been genetically modified to increase the expression of one or more target genes involved in protein production, decrease the expression of one or more target genes involved in protein degradation, express a heterologous gene that affects the protein product, or a combination. The ability to express a polypeptide of interest in a variety of modified host cells provides a rapid and efficient means for determining an optimal host cell for the polypeptide of interest. The desired specification will vary depending on the polypeptide of interest, but includes yield, quality, activity, and the like.

It is recognized that the host cell populations may be modified to express many combinations of nucleic acid sequences that affect the expression levels of endogenous sequences and/or exogenous sequences that facilitate the expression of the polypeptide of interest. In one embodiment, two or more of the host cell populations has been genetically modified to increase the expression of one or more target genes involved in one or more of the proper expression, processing, and/or translocation of a heterologous protein of interest. In another embodiment, the target gene is a protein folding modulator. In another embodiment, the protein folding modulator is selected from the list in Table 1.

In another embodiment, one or more of the host cell populations has been genetically modified to decrease the expression of one or more target genes involved in proteolytic degradation. In another embodiment, the target gene is a protease. In another embodiment, the protease is selected from the list in Table 2.

In one embodiment, nucleotide sequences encoding the proteins of interest are operably linked to a P. fluorescens Sec system secretion signal as described herein. One or more of the strains in the array may express the heterologous protein of interest in a periplasm compartment. In certain embodiments, one or more strains may also secrete the heterologous protein extracellularly through an outer cell wall.

Host cells include eukaryotic cells, including yeast cells, insect cells, mammalian cells, plant cells, etc., and prokaryotic cells, including bacterial cells such as P. fluorescens, E. coli, and the like.

As indicated, the library of host cell populations can be rapidly screened to identify certain strain(s) with improved yield and/or quality of heterologously expressed protein. The strain arrays are useful for screening for improved expression of any protein of interest, including therapeutic proteins, hormones, a growth factors, extracellular receptors or ligands, proteases, kinases, blood proteins, chemokines, cytokines, antibodies and the like.

The invention includes a method of assembling an array of expression systems for testing expression of at least one heterologous protein, said method comprising: placing in separate addressable locations at least 10 nonidentical test expression systems, said at least 10 nonidentical test expression systems each comprising a different combination of a) a Pseudomonad or E. coli host cell population, and b) at least one expression vector encoding the at least one heterologous protein, wherein the array includes at least 5 different host cell populations and at least 2 different expression vectors, and further wherein at least 3 of said at least 5 different host cell populations are deficient in their expression of at least one protease; and wherein at least one of the nonidentical test expression systems overexpresses the at least one heterologous protein.

In embodiments, the at least 2 different expression vectors each encode a different heterologous protein. In other embodiments, the array includes at least 5 different expression vectors, and wherein each of said at least 5 different expression vectors encodes a different heterologous protein. In embodiments, at least one expression vector encodes 2 different heterologous proteins. In other embodiments, at least 20 nonidentical test expression systems are placed in separate addressable locations, and wherein the array includes at least 10 different host cell populations and at least 2 different expression vectors, and further wherein at least 5 of said at least 10 different host cell populations are deficient in their expression of at least one protease. In other embodiments at least 50 nonidentical test expression systems are placed in separate addressable locations, and wherein the array includes at least 20 different host cell populations and at least 3 different expression vectors, and further wherein at least 10 of said at least 20 different host cell populations are deficient in their expression of at least one protease. In related embodiments, the overexpression of the heterologous protein in the at least one nonidentical test expression system is an increase in yield, of about 1.5-fold to an about 100-fold, relative to the yield in an indicator expression system. In other embodiments, the overexpression is a yield of the heterologous protein in the at least one nonidentical test expression system of about 10 mg/liter to about 2000 mg/liter. In related embodiments, the increase in yield is about 1.5-fold to about 2-fold, about 2-fold to about 3-fold, about 3-fold to about 4-fold, about 4-fold to about 5-fold, about 5-fold to about 6 fold, about 6-fold to about 7-fold, about 7-fold to about 8-fold, about 8-fold to about 9-fold, about 9-fold to about 10-fold, about 10-fold to about 15-fold, about 15-fold to about 20-fold, about 20-fold to about 25-fold, about 25-fold to about 30-fold, about 30-fold to about 35-fold, about 35-fold to about 40-fold, about 45-fold to about 50-fold, about 50-fold to about 55-fold, about 55-fold to about 60-fold, about 60-fold to about 65-fold, about 65-fold to about 70-fold, about 70-fold to about 75-fold, about 75-fold to about 80-fold, about 80-fold to about 85-fold, about 85-fold to about 90-fold, about 90-fold to about 95-fold, or about 95-fold to about 100-fold. In other related embodiments, the yield of the heterologous protein is about 10 mg/liter to about 20 mg/liter, about 20 mg/liter to about 50 mg/liter, about 50 mg/liter to about 100 mg/liter, about 100 mg/liter to about 200 mg/liter, about 200 mg/liter to about 300 mg/liter, about 300 mg/liter to about 400 mg/liter, about 400 mg/liter to about 500 mg/liter, about 500 mg/liter to about 600 mg/liter, about 600 mg/liter to about 700 mg/liter, about 700 mg/liter to about 800 mg/liter, about 800 mg/liter to about 900 mg/liter, about 900 mg/liter to about 1000 mg/liter, about 1000 mg/liter to about 1500 mg/liter, or about 1500 mg/liter to about 2000 mg/liter. Included are embodiments wherein the indicator expression system comprises a second nonidentical test expression system in the array or a standard expression system. In other embodiments, the yield of the heterologous protein is a measure of the amount of soluble heterologous protein, the amount of recoverable heterologous protein, the amount of properly processed heterologous protein, the amount of properly folded heterologous protein, the amount of active heterologous protein, and/or the total amount of heterologous protein. The invention includes methods wherein the optimal expression system is selected from among the test expression systems based on the increased yield of the heterologous protein in the test expression system relative to that in the indicator expression system. In certain embodiments, an optimal expression system is selected from among the test expression systems based on the yield of the heterologous protein in the test expression system.

The invention also includes methods for selecting an optimal expression system comprising using the array assembled using the methods of the invention, and an array assembled using the methods of the invention. In embodiments, at least 2 of said at least 5 different expression systems overexpress at least one folding modulator. In other embodiments, the at least one folding modulator is selected from the folding modulators listed herein in Table 1 and Table 2. In embodiments, the at least one folding modulator is expressed from a plasmid. In certain embodiments, at least one host cell population is defective in at least one to about eight proteases. In other embodiments, the at least one to about eight proteases are selected from the proteases listed in Table 1 and Table 2. In embodiments, the methods of the invention include determining the number of cysteine residues in, the presence of clustered prolines in, the requirement of an N terminal methionine for activity of, or the presence of a small amino acid in the plus two position of, the heterologous protein. In certain embodiments, when the heterologous protein has more than two cysteine residues, at least one of said at least 2 different expression systems overexpressing a folding modulator overexpresses a disulfide isomerase/oxidoreductase. In embodiments, the disulfide isomerase/oxidoreductase is encoded on a plasmid. In embodiments, when the heterologous protein has more than four cysteine residues, at least one of said at least 2 different expression vectors encoding the heterologous protein contains a periplasmic secretion leader sequence. In other embodiments, when the heterologous protein has more than four cysteine residues, at least one of said at least 2 different expression vectors encoding the heterologous protein contains a high or medium ribosome binding sequence. In embodiments, said at least one of said at least 2 different expression vectors encoding the heterologous protein and containing a periplasmic secretion leader sequence is included in at least one expression system that overexpresses at least one periplasmic chaperone, and at least one expression system that overexpresses at least one cytoplasmic chaperone. In other embodiments, when the heterologous protein has fewer than four cysteine residues, at least one of said at least 2 different expression vectors encoding the heterologous protein does not contain a periplasmic secretion leader sequence, and further wherein said at least one of said at least 2 different expression vectors encoding the heterologous protein and not containing a periplasmic secretion leader sequence is included in at least one expression system that overexpresses at least one cytoplasmic chaperone. In other embodiments, when clustered prolines are present, at least one expression system that overexpresses at least one 2+ peptidyl-prolyl cis-trans isomerase (PPIase) is included in the array. In certain embodiments, the 2+ peptidyl-prolyl cis-trans isomerase (PPIase) is encoded on a plasmid. In other embodiments, when the N-terminal methionine is required, at least one expression system comprising a host cell population that has at least one defect in at least one methionyl amino peptidase, is included in the array. In embodiments, when a small amino acid is present in the plus two position of the heterologous protein, at least one expression system comprising a host cell population that has at least one defect in at least one amino peptidase, is included in the array.

In embodiments, the small amino acid is selected from the group consisting of: glycine, alanine, valine, serine, threonine, aspartic acid, asparagine, and proline. In embodiments, the heterologous protein is a toxin. In specific embodiments, the toxin is a vertebrate or invertebrate animal toxin, a plant toxin, a bacterial toxin, a fungal toxin, or variant thereof. In other embodiments, the heterologous protein is a cytokine, growth factor or hormone, or receptor thereof. In certain embodiments, the heterologous protein is an antibody or antibody derivative. In specific embodiments, the antibody or antibody derivative is a humanized antibody, modified antibody, nanobody, bispecific antibody, single-chain antibody, Fab, Domain antibody, shark single domain antibody, camelid single domain antibody, linear antibody, diabody, or BiTE molecule. In other embodiments, the heterologous protein is a human therapeutic protein or therapeutic enzyme, a non-natural protein, a fusion protein, a chaperone, a pathogen protein or pathogen-derived antigen, a lipoprotein, a reagent protein, or a biocatalytic enzyme. In embodiments of the invention, at least 10% of the heterologous protein is insoluble when expressed in an indicator strain, or wherein the heterologous protein is predicted to be insoluble using a protein solubility prediction tool.

The invention additionally includes a method for selecting an optimal expression system for overexpressing at least one heterologous protein, said method comprising: assembling an array by placing in separate addressable locations at least 10 nonidentical test expression systems, said at least 10 nonidentical test expression systems each comprising a different combination of a) Pseudomonad or E. coli host cell population, and b) at least one expression vector encoding the at least one heterologous protein, wherein the array includes at least 5 different host cell populations and at least 2 different expression vectors, and further wherein at least 3 of said at least 10 different host cell populations are deficient in their expression of at least one protease; measuring the yield of the heterologous protein expressed; and selecting at least one optimal expression system from among the test expression systems based on the yield of the heterologous protein measured. In embodiments, the yield of the heterologous protein is about 1.5-fold to an about 100-fold higher in the at least one optimal expression system relative to that in an indicator expression system. In other embodiments, the yield of the heterologous protein in the at least one optimal expression system is about 10 mg/liter to about 2000 mg/liter. In certain embodiments, the indicator expression system comprises a second nonidentical test expression system in the array or a standard expression system. In embodiments, the yield of the heterologous protein is a measure of the amount of soluble heterologous protein, the amount of recoverable heterologous protein, the amount of properly processed heterologous protein, the amount of properly folded heterologous protein, the amount of active heterologous protein, and/or the total amount of heterologous protein.

The invention also includes an array of expression systems for testing expression of at least one heterologous protein, said array comprising: at least 10 nonidentical test expression systems in separate addressable locations, said at least 10 nonidentical test expression systems each comprising a different combination of a) a Pseudomonad or E. coli host cell population, and b) at least one expression vector encoding at least one heterologous protein, wherein the array includes at least 5 different host cell populations and at least 2 different expression vectors, and further wherein at least 3 of said at least 5 different host cell populations are deficient in their expression of at least one protease; and wherein at least one of the nonidentical test expression systems overexpresses the heterologous protein.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A depicts plasmid pDOW1261-2 used for engineering genomic deletion in P. fluorescens. FIG. 1B is a schematic drawing of the constructions of a gene X deletion.

FIG. 2 is a Western blot analysis of soluble cells fractions prepared at 0 and 24 hours post-induction (I0 and I24, respectively) in Δprc1, ΔdegP2, ΔLa2 and the grpEdnaKJ co-expression strains (Example 6). The top arrows point to the fully assembled monoclonal antibody in the co-expressed strains but not in the control (DC440). r=recombinant; n-r=nonrecombinant.

FIG. 3 shows growth curves for P. fluorescens (filled symbols) and E. coli (open symbols) expression clones observed during growth in a 96-well format. Elapsed fermentation time in hours is shown on the X-axis and optical density measured at 600 nm (A₆₀₀) is shown on the Y-axis. The arrow indicates time of induction of P. fluorescens cultures.

FIG. 4 shows SDS-PAGE (A) and Western blot (B) analysis of analyses of soluble (S) and insoluble (I) samples following 24 hours induction of E. coli (E) or P. fluorescens (P) cultures. Molecular weight markers are indicated in the first lane. Proteins expressed are indicated at the bottom of the gel image.

FIG. 5 provides the sequences of the elements of SEQ ID NOS: 138-157, including open reading frames for folding modulators and proteases.

FIG. 6 provides sequences, including leader sequences, also provided herein in the sequence listing. These sequences are disclosed in U.S. Patent App. Pub. No. 2008/0193974, “Bacterial leader sequences for increased expression.”

FIG. 7 provides sequences, including leader sequences, also provided herein in the sequence listing as SEQ ID NOS:208-327. These sequences are disclosed in U.S. Patent App. Pub. No. US2006/0008877, “Expression systems with Sec-secretion.”

DETAILED DESCRIPTION

The present inventions now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the invention are shown. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements.

Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings.

Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the invention. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.

Overview

Compositions and methods for identifying an optimal host strain, e.g, a Pseudomonas fluorescens host strain, for producing high levels of properly processed heterologous polypeptides in a host cell are provided. In particular, a library (or “array”) of host strains is provided, wherein each strain (or “population of host cells”) in the library has been genetically modified to modulate the expression of one or more target genes in the host cell. An “optimal host strain” or “optimal expression system” can be identified or selected based on the quantity, quality, and/or location of the expressed protein of interest compared to other populations of phenotypically distinct host cells in the array. Thus, an optimal host strain is the strain that produces the polypeptide of interest according to a desired specification. While the desired specification will vary depending on the polypeptide being produced, the specification includes the quality and/or quantity of protein, whether the protein is sequestered or secreted, protein folding, and the like. For example, the optimal host strain or optimal expression system produces a yield, characterized by the amount of soluble heterologous protein, the amount of recoverable heterologous protein, the amount of properly processed heterologous protein, the amount of properly folded heterologous protein, the amount of active heterologous protein, and/or the total amount of heterologous protein, of a certain absolute level or a certain level relative to that produced by an indicator strain, i.e., a strain used for comparison.

“Heterologous,” “heterologously expressed,” or “recombinant” generally refers to a gene or protein that is not endogenous to the host cell or is not endogenous to the location in the native genome in which it is present, and has been added to the cell by infection, transfection, microinjection, electroporation, microprojection, or the like.

One or more of the host cell populations in the array is modified to modulate the expression of one or more target genes in the host cell. By “target gene” is intended a gene that affects heterologous protein production in a host cell. Target genes that affect heterologous protein production include genes encoding proteins that modulate expression, activity, solubility, translocation, proteolytic degradation and/or cleavage of the heterologous protein. For example, a target gene may encode at least one of a host cell protease, a protein folding modulator, a transcription factor, a translation factor, a secretion modulator, or any other protein involved in the proper transcription, translation, processing, and/or translocation of a heterologous protein of interest. A “target protein” refers to the protein or polypeptide resulting from expression of the target gene. Expression and/or activity of a target gene or genes is increased or decreased, depending on the function of the target gene or protein. For example, expression of one or more host cell proteases may be decreased, whereas expression of one or more protein folding modulators may be increased.

The arrays described herein are useful for rapidly identifying an optimal host cell for production of a heterologous protein or peptide of interest. Heterologous protein production often leads to the formation of insoluble or improperly folded proteins, which are difficult to recover and may be inactive. Furthermore, the presence of specific host cell proteases may degrade the protein of interest and thus reduce the final yield. There is no single host cell population that will optimally produce all polypeptides or proteins of interest. Thus, using the compositions and methods of the invention, an optimal host cell can be rapidly and efficiently identified from the library of modified cell populations. The optimal host strain can then be used to produce sufficient amounts of the protein of interest or for commercial production. Likewise, a host strain can be modified for expression of the protein of interest based on the optimal host strain.

In one embodiment, the method includes obtaining an array comprising at least a first and a second population of P. fluorescens cells, wherein each population is selected from the group consisting of (i) a population of P. fluorescens cells that has been genetically modified to reduce the expression of at least target gene involved in protein degradation; (ii) a population of P. fluorescens cells that has been genetically modified to increase the expression of at least one target gene involved in protein production; and, (iii) a population of P. fluorescens cells that has been genetically modified to reduce the expression of at least one target gene involved in protein degradation and to increase the expression of at least one target gene involved in protein production; introducing into at least one cell of each population an expression construct comprising at least one gene encoding at least one heterologous protein of interest; maintaining said cells under conditions sufficient for the expression of said protein of interest in at least one population of cells; and selecting the optimal population of cells in which the heterologous protein of interest is produced; wherein each population in the array is non-identical and wherein each population is physically separate from one from another; wherein the heterologous protein of interest exhibits one or more of improved expression, improved activity, improved solubility, improved translocation, or reduced proteolytic degradation or cleavage in the optimal population of cells compared to other populations in the array.

The array may further comprise a population of host cells (e.g., P. fluorescens host cells) that has not been genetically modified to alter the expression of a host cell protease or a protein folding modulator. This population may be a wild-type strain, or may be a strain that has been genetically modified to alter the expression of or more genes not involved in protein production, processing, or translocation (e.g., may be genetically modified to express, for example, a selectable marker gene).

In one embodiment, each population of P. fluorescens host cells is phenotypically distinct (i.e., “non-identical”) one from another. By “phenotypically distinct” is intended that each population produces a measurably different amount of one or more target proteins. In this embodiment, each strain has been genetically modified to alter the expression of one or more different target genes. Where the expression of more than one target gene is modulated in a population of host cells, then the combination of target genes is phenotypically distinct from other populations in the library. An array comprising a plurality of phenotypically distinct populations of host cells according to the present invention is one that provides a diverse population from which to select one or more strains useful for producing a heterologous protein or peptide of interest. It will be understood by one of skill in the art that such an array may also comprise replicates (e.g., duplicates, triplicates, etc.) of any one or more populations of host cells.

In embodiments, structural characteristics of the recombinant protein guide the selection of expression vector elements. The expression vector elements can in turn influence selection of the host cell population. For example, a recombinant protein having multiple cysteine residues can have a propensity to misfold improper due to disulfide mispairing. Using the methods of the present invention, an array that includes at least one expression vector having a periplasmic secretion leader is assembled, and in turn that expression vector is paired with a host cell population that overexpresses a periplasmic chaperone. The host strain element thus can act synergistically with the vector element to increase expression of the recombinant protein. Thus, in embodiments, an array of the present invention is assembled using different combinations of potentially synergistic expression vector and host cell elements.

In embodiments, a heterologous protein containing more than one disulfide bond, or more than two cysteine residues, can be screened in expression systems wherein the host strain is, e.g., a disulfide isomerase/oxidoreductase pathway overexpressor. In addition to the number of cysteine residues available to form disulfide bonds, a heterologous protein can be evaluated to determine the presence of clustered prolines, the requirement of an N terminal methionine for activity, or the presence of a small amino acid in the plus two position. In embodiments, identification of the presence of clustered prolines or several prolines within relatively close proximity indicates the use of a 2+ peptidyl-prolyl cis-trans isomerase (PPIase) overexpression host cell population. In other embodiments, a host cell population that has at least one defect in at least one methionyl amino peptidase is included in the array when the heterologous protein is determined to require an N-terminal methionine. In still other embodiments, a host cell population that has at least one defect in at least one amino peptidase is included in an expression system of the array when the presence of a small amino acid in the plus two position of the heterologous protein is identified.

The heterologous protein can also be evaluated for a propensity for protease degradation, and a host cell populations having one or more protease mutations used in the array. Furthermore, if a cleavage site for a specific protease is identified, a host having a mutation in the protease(s) which cleaves at that site can be included in the array. Useful host cell populations can contain multiple protease mutations, multiple folding modulators, or both protease mutations and folding modulators. In embodiments, a host cell population that has at least one to at least eight different protease mutations is used in an expression system of the array.

Variation of the expression systems of the invention at multiple interdependent levels allows fine-tuning of expression, which in conjunction with rapid screening capabilities provides a powerful tool for identifying overexpression systems for any protein.

Arrays

Provided herein is an array of host cell populations (i.e. “strain array”) which can be rapidly screened to identify certain strain(s) with improved yield and/or quality of heterologous protein. As used herein, the term “strain array” refers to a plurality of addressed or addressable locations (e.g., wells, such as deep well or microwells). The location of each of the microwells or groups of microwells in the array is typically known, so as to allow for identification of the optimal host cell for expression of the heterologous protein of interest.

The strain array comprises a plurality of phenotypically distinct host strains. The arrays may be low-density arrays or high-density arrays and may contain about 2 or more, about 4 or more, about 8 or more, about 12 or more, about 16 or more, about 20 or more, about 24 or more, about 32 or more, about 40 or more, about 48 or more, about 64 or more, about 72 or more, about 80 or more, about 96 or more, about 192 or more, about 384 or more host cell populations.

The host cell populations of the invention can be maintained and/or screened in a multi-well or deep well vessel. The vessel may contain any desired number of wells, however, a miniaturized cell culture microarray platform is useful for screening each population of host cells individually and simultaneously using minimal reagents and a relatively small number of cells. A typical multi-well, microtiter vessel useful in this assay is a multi-well plate including, without limitation, 10-well plates, 28-well plates, 96-well plates, 384-well plates, and plates having greater than 384 wells. Alternatively, an array of tubes, holders, cartridges, minitubes, microfuge tubes, cryovials, square well plates tubes, plates, slants, or culture flasks may also be used, depending on the volume desired.

The vessel may be made of any material suitable for culturing and/or screening a host cell of interest, e.g., Pseudomonas. For example, the vessel can be a material that can be easily sterilized such as plastic or other artificial polymer material, so long as the material is biocompatible. Any number of materials can be used, including, but not limited to, polystyrene; polypropylene; polyvinyl compounds (e.g. polyvinylchloride); polycarbonate (PVC); polytetrafluoroethylene (PTFE); polyglycolic acid (PGA); cellulose; glass, fluoropolymers, fluorinated ethylene propylene, polyvinylidene, polydimethylsiloxane, silicon, and the like.

Automated transformation of cells and automated colony pickers will facilitate rapid screening of desired cells. The arrays may be created and/or screened using a spotter device (e.g., automated robotic devices) as known in the art.

Target Genes

The strain array of the present invention comprises a plurality of phenotypically and genotypically distinct host cell populations, wherein each population in the array has been genetically modified to modulate the expression of one or more target genes in the host cell. By “target gene” is intended a gene that affects heterologous protein production in a host cell. A target gene may encode a host cell protease or an endogenous or exogenous protein folding modulator, transcription factor, translation factor, secretion modulator, or any other gene involved in the proper expression, processing, and/or translocation of a heterologous protein of interest. A “target protein” refers to the protein or polypeptide resulting from expression of the target gene. Expression and/or activity of a target gene or genes is increased or decreased, depending on the function of the target gene or protein. A target gene can be endogenous to the host cell, or can be a gene that is heterologously expressed in each of the host cell populations in the array.

In one embodiment, the target gene or genes is at least one protein folding modulator, putative protein folding modulator, or a cofactor or subunit of a folding modulator. In some embodiments, the target gene or genes can be selected from a chaperone protein, a foldase, a peptidyl prolyl isomerase and a disulfide bond isomerase. In some embodiments, the target gene or genes can be selected from htpG, cbpA, dnaJ, dnaK and fkbP. Exemplary protein folding modulators from P. fluorescens are listed in Table 1.

In other embodiments, the target gene comprises at least one putative protease, a protease-like protein, or a cofactor or subunit of a protease. For example, the target gene or genes can be a serine, threonine, cysteine, aspartic or metallopeptidase. In one embodiment, the target gene or genes can be selected from hslV, hslU, clpA, clpB and clpX. The target gene can also be a cofactor of a protease. Exemplary proteases from P. fluorescens are listed in Table 2. Proteases from a variety of organisms can be found in the MEROPS Peptidase Database maintained by the Welcome Trust Sanger Institute, Cambridge, UK (Rawlings et. al., 2006, Nucleic Acids Research 34 (Database issue): D270-2).

Protein Folding Modulators

Another major obstacle in the production of heterologous proteins in host cells is that the cell often is not adequately equipped to produce either soluble or active protein. While the primary structure of a protein is defined by its amino acid sequence, the secondary structure is defined by the presence of alpha helices or beta sheets, and the ternary structure by covalent bonds between adjacent protein stretches, such as disulfide bonds. When expressing heterologous proteins, particularly in large-scale production, the secondary and tertiary structure of the protein itself is of critical importance. Any significant change in protein structure can yield a functionally inactive molecule, or a protein with significantly reduced biological activity. In many cases, a host cell expresses protein folding modulators (PFMs) that are necessary for proper production of active heterologous protein. However, at the high levels of expression generally required to produce usable, economically satisfactory biotechnology products, a cell often cannot produce enough native protein folding modulator or modulators to process the heterologously-expressed protein.

In certain expression systems, overproduction of heterologous proteins can be accompanied by their misfolding and segregation into insoluble aggregates. In bacterial cells these aggregates are known as inclusion bodies. In E. coli, the network of folding modulators/chaperones includes the Hsp70 family. The major Hsp70 chaperone, DnaK, efficiently prevents protein aggregation and supports the refolding of damaged proteins. The incorporation of heat shock proteins into protein aggregates can facilitate disaggregation. However, proteins processed to inclusion bodies can, in certain cases, be recovered through additional processing of the insoluble fraction. Proteins found in inclusion bodies typically have to be purified through multiple steps, including denaturation and renaturation. Typical renaturation processes for inclusion body targeted proteins involve attempts to dissolve the aggregate in concentrated denaturant and subsequent removal of the denaturant by dilution. Aggregates are frequently formed again in this stage. The additional processing adds cost, there is no guarantee that the in vitro refolding will yield biologically active product, and the recovered proteins can include large amounts of fragment impurities.

The recent realization that in vivo protein folding is assisted by molecular chaperones, which promote the proper isomerization and cellular targeting of other polypeptides by transiently interacting with folding intermediates, and by foldases, which accelerate rate-limiting steps along the folding pathway, has provided additional approaches to combat the problem of inclusion body formation (see for e.g. Thomas J G et al. (1997) Appl Biochem Biotechnol 66:197-238).

In certain cases, the overexpression of chaperones has been found to increase the soluble yields of aggregation-prone proteins (see Baneyx, F. (1999) Curr. Opin. Biotech. 10:411-421 and references therein). The beneficial effect associated with an increase in the intracellular concentration of these chaperones appears highly dependent on the nature of the overproduced protein, and may not require overexpression of the same protein folding modulator(s) for all heterologous proteins.

Protein folding modulators, including chaperones, disulfide bond isomerases, and peptidyl-prolyl cis-trans isomerases (PPIases) are a class of proteins present in all cells which aid in the folding, unfolding and degradation of nascent polypeptides.

Chaperones act by binding to nascent polypeptides, stabilizing them and allowing them to fold properly. Proteins possess both hydrophobic and hydrophilic residues, the former are usually exposed on the surface while the latter are buried within the structure where they interact with other hydrophilic residues rather than the water which surrounds the molecule. However in folding polypeptide chains, the hydrophilic residues are often exposed for some period of time as the protein exists in a partially folded or misfolded state. It is during this time when the forming polypeptides can become permanently misfolded or interact with other misfolded proteins and form large aggregates or inclusion bodies within the cell. Chaperones generally act by binding to the hydrophobic regions of the partially folded chains and preventing them from misfolding completely or aggregating with other proteins. Chaperones can even bind to proteins in inclusion bodies and allow them to disaggregate (Ranson et. al. 1998). The GroES/EL, DnaKJ, Clp, Hsp90 and SecB families of folding modulators are all examples of proteins with chaperone like activity.

Another important type of folding modulator is the disulfide bond isomerases. These proteins catalyze a very specific set of reactions to help folding polypeptides form the proper intra-protein disulfide bonds. Any protein that has more than two cysteines is at risk of forming disulfide bonds between the wrong residues. The disulfide bond formation family consists of the Dsb proteins which catalyze the formation of disulfide bonds in the non-reducing environment of the periplasm. When a periplasmic polypeptide misfolds disulfide bond isomerase, DsbC is capable of rearranging the disulfide bonds and allowing the protein to reform with the correct linkages.

The proline residue is unique among amino acids in that the peptidyl bond immediately preceding it can adopt either a cis or trans conformation. For all other amino acids this is not favored due to steric hindrance. Peptidyl-prolyl cis-trans isomerases (PPIases) catalyze the conversion of this bond from one form to the other. This isomerization may aid in protein folding, refolding, assembly of subunits and trafficking in the cell (Dolinski, et. al. 1997).

In addition to the general chaperones which seem to interact with proteins in a non-specific manner, there are also chaperones which aid in the folding of specific targets. These protein-specific chaperones form complexes with their targets, preventing aggregation and degradation and allowing time for them to assemble into multi-subunit structures. The PapD chaperone is one well known example of this type (Lombardo et. al. 1997).

Folding modulators also include, for example, HSP70 proteins, HSP110/SSE proteins, HSP40 (DNAJ-related) proteins, GRPE-like proteins, HSP90 proteins, CPN60 and CPN10 proteins, Cytosolic chaperoning, HSP100 proteins, Small HSPs, Calnexin and calreticulin, PDI and thioredoxin-related proteins, Peptidyl-prolyl isomerases, Cyclophilin PPIases, FK-506 binding proteins, Parvulin PPIases, Individual chaperoning, Protein specific chaperones, or intramolecular chaperones. Folding modulators are generally described in “Guidebook to Molecular Chaperones and Protein-Folding Catalysts” (1997) ed. M. Gething, Melbourne University, Australia.

The best characterized molecular chaperones in the cytoplasm of E. coli are the ATP-dependent DnaK-DnaJ-GrpE and GroEL-GroES systems. Based on in vitro studies and homology considerations, a number of additional cytoplasmic proteins have been proposed to function as molecular chaperones in E. coli. These include ClpB, HtpG and IbpA/B, which, like DnaK-DnaJ-GrpE and GroEL-GroES, are heat-shock proteins (Hsps) belonging to the stress regulon. The trans conformation of X-Pro bonds is energetically favored in nascent protein chains; however, approximately 5% of all prolyl peptide bonds are found in a cis conformation in native proteins. The trans to cis isomerization of X-Pro bonds is rate limiting in the folding of many polypeptides and is catalyzed in vivo by peptidyl prolyl cis/trans isomerases (PPIases). Three cytoplasmic PPIases, SlyD, SlpA and trigger factor (TF), have been identified to date in E. coli. TF, a 48 kDa protein associated with 505 ribosomal subunits that has been postulated to cooperate with chaperones in E. coli to guarantee proper folding of newly synthesized proteins. At least five proteins (thioredoxins 1 and 2, and glutaredoxins 1, 2 and 3, the products of the trxA, trxC, grxA, grxB and grxC genes, respectively) are involved in the reduction of disulfide bridges that transiently arise in cytoplasmic enzymes. Thus, target genes can be disulfide bond forming proteins or chaperones that allow proper disulfide bond formation.

TABLE 1 P. fluorescens strain MB214 protein folding modulators ORF ID GENE FUNCTION FAMILY LOCATION GroES/EL RXF02095.1 groES Chaperone Hsp10 Cytoplasmic RXF06767.1:: groEL Chaperone Hsp60 Cytoplasmic Rxf02090 RXF01748.1 ibpA Small heat-shock protein (sHSP) IbpA Hsp20 Cytoplasmic PA3126; Acts as a holder for GroESL folding RXF03385.1 hscB Chaperone protein hscB Hsp20 Cytoplasmic Hsp70 (DnaK/J) RXF05399.1 dnaK Chaperone Hsp70 Periplasmic RXF06954.1 dnaK Chaperone Hsp70 Cytoplasmic RXF03376.1 hscA Chaperone Hsp70 Cytoplasmic RXF03987.2 cbpA Curved dna-binding protein, dnaJ like activity Hsp40 Cytoplasmic RXF05406.2 dnaJ Chaperone protein dnaJ Hsp40 Cytoplasmic RXF03346.2 dnaJ Molecular chaperones (DnaJ family) Hsp40 Non-secretory RXF05413.1 grpE heat shock protein GrpE PA4762 GrpE Cytoplasmic Hsp100 (Clp/Hsl) RXF04587.1 clpA atp-dependent clp protease atp-binding subunit Hsp100 Cytoplasmic clpA RXF08347.1 clpB ClpB protein Hsp100 Cytoplasmic RXF04654.2 clpX atp-dependent clp protease atp-binding subunit Hsp100 Cytoplasmic clpX RXF04663.1 clpP atp-dependent Clp protease proteolytic subunit MEROPS Cytoplasmic (ec 3.4.21.92) peptidase family S14 RXF01957.2 hslU atp-dependent hsl protease atp-binding subunit Hsp100 Cytoplasmic hslU RXF01961.2 hslV atp-dependent hsl protease proteolytic subunit MEROPS Cytoplasmic peptidase subfamily T1B Hsp33 RXF04254.2 yrfI 33 kDa chaperonin (Heat shock protein 33 Hsp33 Cytoplasmic homolog) (HSP33). Hsp90 RXF05455.2 htpG Chaperone protein htpG Hsp90 Cytoplasmic SecB RXF02231.1 secB secretion specific chaperone SecB SecB Non-secretory Disulfide Bond Isomerases RXF07017.2 dsbA disulfide isomerase DSBA oxido- Cytoplasmic reductase RXF08657.2 dsbA/ disulfide isomerase DSBA oxido- Cytoplasmic dsbC/ reductase dsbG/ fernA RXF01002.1 dsbA/ disulfide isomerase DSBA oxido- Periplasmic dsbC reductase/ Thioredoxin RXF03307.1 dsbC disulfide isomerase Glutaredoxin/ Periplasmic Thioredoxin RXF04890.2 dsbG disulfide isomerase Glutaredoxin/ Periplasmic Thioredoxin RXF03204.1 dsbB Disulfide bond formation protein B (Disulfide DSBA oxido- Periplasmic oxidoreductase). reductase RXF04886.2 dsbD Thiol:disulfide interchange protein dsbD DSBA oxido- Periplasmic reductase Peptidyl-prolyl cis-trans isomerases RXF03768.1 ppiA Peptidyl-prolyl cis-trans isomerase A (ec 5.2.1.8) PPIase: Periplasmic cyclophilin type RXF05345.2 ppiB Peptidyl-prolyl cis-trans isomerase B. PPIase: Cytoplasmic cyclophilin type RXF06034.2 fklB Peptidyl-prolyl cis-trans isomerase FklB. PPIase: OuterMembrane FKBP type RXF06591.1 fklB/ fk506 binding protein Peptidyl-prolyl cis-trans PPIase: Periplasmic fkbP isomerase (EC 5.2.1.8) FKBP type RXF05753.2 fklB; Peptidyl-prolyl cis-trans isomerase (ec 5.2.1.8) PPIase: OuterMembrane fkbP FKBP type RXF01833.2 slyD Peptidyl-prolyl cis-trans isomerase SlyD. PPIase: Non-secretory FKBP type RXF04655.2 tig Trigger factor, ppiase (ec 5.2.1.8) PPIase: Cytoplasmic FKBP type RXF05385.1 yaad Probable FKBP-type 16 kDa peptidyl-prolyl cis- PPIase: Non-secretory trans isomerase (EC 5.2.1.8) (PPiase) FKBP type (Rotamase). RXF00271.1 Peptidyl-prolyl cis-trans isomerase (ec 5.2.1.8) PPIase: Non-secretory FKBP type pili assembly chaperones (papD like) RXF06068.1 cup Chaperone protein cup pili assembly Periplasmic papD RXF05719.1 ecpD Chaperone protein ecpD pili assembly Signal peptide papD RXF05319.1 ecpD Hnr protein pili assembly Periplasmic chaperone RXF03406.2 ecpD; Chaperone protein ecpD pili assembly Signal peptide csuC papD RXF04296.1 ecpD; Chaperone protein ecpD pili assembly Periplasmic cup papD RXF04553.1 ecpD; Chaperone protein ecpD pili assembly Periplasmic cup papD RXF04554.2 ecpD; Chaperone protein ecpD pili assembly Periplasmic cup papD RXF05310.2 ecpD; Chaperone protein ecpD pili assembly Periplasmic cup papD RXF05304.1 ecpD; Chaperone protein ecpD pili assembly Periplasmic cup papD RXF05073.1 gltF Gram-negative pili assembly chaperone pili assembly Signal peptide periplasmic function papD Type II Secretion Complex RXF05445.1 YacJ Histidinol-phosphate aminotransferase (ec Class-II pyridoxal- Membrane 2.6.1.9) phosphate-dependent aminotransferase family. Histidinol- phosphate amino- transferase subfamily. RXF05426.1 SecD Protein translocase subunit secd Type II Membrane secretion complex RXF05432.1 SecF protein translocase subunit secf Type II Membrane secretion complex Disulfide Bond Reductases RXF08122.2 trxC Thioredoxin 2 Disulfide Cytoplasmic Bond Reductase RXF06751.1 Gor Glutathione reductase (EC 1.8.1.7) (GR) (GRase) Disulfide Cytoplasmic PA2025 Bond Reductase RXF00922.1 gshA Glutamate--cysteine ligase (ec 6.3.2.2) PA5203 Disulfide Cytoplasmic Bond Reductase

Protease

Unwanted degradation of heterologously-expressed protein presents an obstacle to the efficient use of certain expression systems. When a cell is modified to produce large quantities of a target protein, the cell is placed under stress and often reacts by inducing or suppressing other proteins. The stress that a host cell undergoes during production of heterologous proteins can increase expression of, for example, specific proteins or cofactors to cause degradation of the overexpressed heterologous protein. The increased expression of compensatory proteins can be counterproductive to the goal of expressing high levels of active, full-length heterologous protein. Decreased expression or lack of adequate expression of other proteins can cause misfolding and aggregation of the heterologously-expressed protein. While it is known that a cell under stress will change its profile of protein expression, not all heterologously expressed proteins will modulate expression of the same proteins in a particular host cell.

Thus, the optimal host strain, e.g., P. fluorescens host strain, can be identified using an array comprising a plurality of host cell populations that have been genetically engineered to decrease the expression of one or more protease enzymes. In one embodiment, one or more host cell populations is modified by reducing the expression of, inhibiting or removing at least one protease from the genome. The modification can also be to more than one protease. In a related embodiment, the cell is modified by reducing the expression of a protease cofactor or protease protein. In another embodiment, the host cell is modified by inhibition of a promoter for a protease or related protein, which can be a native promoter. Alternatively, the gene modification can be to modulate a protein homologous to the target gene.

The array comprising the modified host strains can be screened by expressing the heterologous protein(s) of interest and assessing the quality and/or quantity of protein production as discussed infra. Alternatively, an isolate of the heterologous protein of interest can be independently incubated with lysate collected from each of the protease-deficient host cell populations and the level of proteolytic degradation can be used to identify the optimal host cell. In this embodiment, the optimal host cell population is that which results in the least amount of heterologous protein degradation. Thus, in one embodiment, lysate from the optimal host cell population can be degraded by less than about 50% of the heterologous protein, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 10%, less than about 5%, less than about 4%, about 3%, about 2%, about 1%, or less of the protein.

Exemplary target protease genes include those proteases classified as Aminopeptidases; Dipeptidases; Dipeptidyl-peptidases and tripeptidyl peptidases; Peptidyl-dipeptidases; Serine-type carboxypeptidases; Metallocarboxypeptidases; Cysteine-type carboxypeptidases; Omegapeptidases; Serine proteinases; Cysteine proteinases; Aspartic proteinases; Metallo proteinases; or Proteinases of unknown mechanism.

Aminopeptidases include cytosol aminopeptidase (leucyl aminopeptidase), membrane alanyl aminopeptidase, cystinyl aminopeptidase, tripeptide aminopeptidase, prolyl aminopeptidase, arginyl aminopeptidase, glutamyl aminopeptidase, x-pro aminopeptidase, bacterial leucyl aminopeptidase, thermophilic aminopeptidase, clostridial aminopeptidase, cytosol alanyl aminopeptidase, lysyl aminopeptidase, x-trp aminopeptidase, tryptophanyl aminopeptidase, methionyl aminopeptidas, d-stereospecific aminopeptidase, aminopeptidase ey. Dipeptidases include x-his dipeptidase, x-arg dipeptidase, x-methyl-his dipeptidase, cys-gly dipeptidase, glu-glu dipeptidase, pro-x dipeptidase, x-pro dipeptidase, met-x dipeptidase, non-stereospecific dipeptidase, cytosol non-specific dipeptidase, membrane dipeptidase, beta-ala-his dipeptidase. Dipeptidyl-peptidases and tripeptidyl peptidases include dipeptidyl-peptidase i, dipeptidyl-peptidase ii, dipeptidyl peptidase iii, dipeptidyl-peptidase iv, dipeptidyl-dipeptidase, tripeptidyl-peptidase I, tripeptidyl-peptidase II. Peptidyl-dipeptidases include peptidyl-dipeptidase a and peptidyl-dipeptidase b. Serine-type carboxypeptidases include lysosomal pro-x carboxypeptidase, serine-type D-ala-D-ala carboxypeptidase, carboxypeptidase C, carboxypeptidase D. Metallocarboxypeptidases include carboxypeptidase a, carboxypeptidase B, lysine(arginine) carboxypeptidase, gly-X carboxypeptidase, alanine carboxypeptidase, muramoylpentapeptide carboxypeptidase, carboxypeptidase h, glutamate carboxypeptidase, carboxypeptidase M, muramoyltetrapeptide carboxypeptidase, zinc d-ala-d-ala carboxypeptidase, carboxypeptidase A2, membrane pro-x carboxypeptidase, tubulinyl-tyr carboxypeptidase, carboxypeptidase t. Omegapeptidases include acylaminoacyl-peptidase, peptidyl-glycinamidase, pyroglutamyl-peptidase I, beta-aspartyl-peptidase, pyroglutamyl-peptidase II, n-formylmethionyl-peptidase, pteroylpoly-[gamma]-glutamate carboxypeptidase, gamma-glu-X carboxypeptidase, acylmuramoyl-ala peptidase. Serine proteinases include chymotrypsin, chymotrypsin c, metridin, trypsin, thrombin, coagulation factor Xa, plasmin, enteropeptidase, acrosin, alpha-lytic protease, glutamyl, endopeptidase, cathepsin G, coagulation factor viia, coagulation factor ixa, cucumisi, prolyl oligopeptidase, coagulation factor xia, brachyurin, plasma kallikrein, tissue kallikrein, pancreatic elastase, leukocyte elastase, coagulation factor xiia, chymase, complement component c1r55, complement component c1s55, classical-complement pathway c3/c5 convertase, complement factor I, complement factor D, alternative-complement pathway c3/c5 convertase, cerevisin, hypodermin C, lysyl endopeptidase, endopeptidase 1a, gamma-reni, venombin ab, leucyl endopeptidase, tryptase, scutelarin, kexin, subtilisin, oryzin, endopeptidase k, thermomycolin, thermitase, endopeptidase SO, T-plasminogen activator, protein C, pancreatic endopeptidase E, pancreatic elastase ii, IGA-specific serine endopeptidase, U-plasminogen, activator, venombin A, furin, myeloblastin, semenogelase, granzyme A or cytotoxic T-lymphocyte proteinase 1, granzyme B or cytotoxic T-lymphocyte proteinase 2, streptogrisin A, treptogrisin B, glutamyl endopeptidase II, oligopeptidase B, limulus clotting factor c, limulus clotting factor, limulus clotting enzyme, omptin, repressor lexa, bacterial leader peptidase I, togavirin, flavirin. Cysteine proteinases include cathepsin B, papain, ficin, chymopapain, asclepain, clostripain, streptopain, actinide, cathepsin 1, cathepsin H, calpain, cathepsin t, glycyl, endopeptidase, cancer procoagulant, cathepsin S, picornain 3C, picornain 2A, caricain, ananain, stem bromelain, fruit bromelain, legumain, histolysain, interleukin 1-beta converting enzyme. Aspartic proteinases include pepsin A, pepsin B, gastricsin, chymosin, cathepsin D, neopenthesin, renin, retropepsin, pro-opiomelanocortin converting enzyme, aspergillopepsin I, aspergillopepsin II, penicillopepsin, rhizopuspepsin, endothiapepsin, mucoropepsin, candidapepsin, saccharopepsin, rhodotorulapepsin, physaropepsin, acrocylindropepsin, polyporopepsin, pycnoporopepsin, scytalidopepsin a, scytalidopepsin b, xanthomonapepsin, cathepsin e, barrierpepsin, bacterial leader peptidase I, pseudomonapepsin, plasmepsin. Metallo proteinases include atrolysin a, microbial collagenase, leucolysin, interstitial collagenase, neprilysin, envelysin, iga-specific metalloendopeptidase, procollagen N-endopeptidase, thimet oligopeptidase, neurolysin, stromelysin 1, meprin A, procollagen C-endopeptidase, peptidyl-lys metalloendopeptidase, astacin, stromelysin, 2, matrilysin gelatinase, aeromonolysin, pseudolysin, thermolysin, bacillolysin, aureolysin, coccolysin, mycolysin, beta-lytic metalloendopeptidase, peptidyl-asp metalloendopeptidase, neutrophil collagenase, gelatinase B, leishmanolysin, saccharolysin, autolysin, deuterolysin, serralysin, atrolysin B, atrolysin C, atroxase, atrolysin E, atrolysin F, adamalysin, horrilysin, ruberlysin, bothropasin, bothrolysin, ophiolysin, trimerelysin I, trimerelysin II, mucrolysin, pitrilysin, insulysin, O-syaloglycoprotein endopeptidase, russellysin, mitochondrial, intermediate, peptidase, dactylysin, nardilysin, magnolysin, meprin B, mitochondrial processing peptidase, macrophage elastase, choriolysin, toxilysin. Proteinases of unknown mechanism include thermopsin and multicatalytic endopeptidase complex.

Certain proteases can have both protease and chaperone-like activity. When these proteases are negatively affecting protein yield and/or quality it can be useful to delete them, and they can be overexpressed when their chaperone activity may positively affect protein yield and/or quality. These proteases include, but are not limited to: Hsp100 (Clp/Hsl) family members RXF04587.1 (clpA), RXF08347.1, RXF04654.2 (clpX), RXF04663.1, RXF01957.2 (hslU), RXF01961.2 (hslV); Peptidyl-prolyl cis-trans isomerase family member RXF05345.2 (ppiB); Metallopeptidase M20 family member RXF04892.1 (aminohydrolase); Metallopeptidase M24 family members RXF04693.1 (methionine aminopeptidase) and RXF03364.1 (methionine aminopeptidase); and Serine Peptidase S26 signal peptidase I family member RXF01181.1 (signal peptidase).

TABLE 2 P. fluorescens strain MB214 proteases Family ORF ID Gene Function Location Aspartic Peptidases A8 (signal peptidase II family) RXF05383.2 Lipoprotein signal peptidase (ec Cytoplasmic 3.4.23.36) Membrane A24 (type IV prepilin peptidase RXF05379.1 type 4 prepilin peptidase pild (ec Cytoplasmic family) 3.4.99.—) Membrane Cysteine Peptidases C15 (pyroglutamyl peptidase I RXF02161.1 Pyrrolidone-carboxylate peptidase Cytoplasmic family) (ec 3.4.19.3) C40 RXF01968.1 invasion-associated protein, P60 Signal peptide RXF04920.1 invasion-associated protein, P60 Cytoplasmic RXF04923.1 phosphatase-associated protein Signal peptide papq C56 (PfpI endopeptidase family) RXF01816.1 protease I (ec 3.4.—.—) Non-secretory Metallopeptidases M1 RXF08773.1 Membrane alanine aminopeptidase Non-secretory (ec 3.4.11.2) M3 RXF00561.2 prlC Oligopeptidase A (ec 3.4.24.70) Cytoplasmic RXF04631.2 Zn-dependent oligopeptidases Cytoplasmic M4 (thermolysin family) RXF05113.2 Extracellular metalloprotease Extracellular precursor (ec 3.4.24.—) M41 (FtsH endopeptidase family) RXF05400.2 Cell division protein ftsH (ec Cytoplasmic 3.4.24.—) Membrane M10 RXF04304.1 Serralysin (ec 3.4.24.40) Extracellular RXF04500.1 Serralysin (ec 3.4.24.40) Extracellular RXF01590.2 Serralysin (ec 3.4.24.40) Extracellular RXF04497.2 Serralysin (ec 3.4.24.40) Extracellular RXF04495.2 Serralysin (ec 3.4.24.40) Extracellular RXF02796.1 Serralysin (ec 3.4.24.40) Extracellular M14 (carboxypeptidase A family) RXF09091.1 Zinc-carboxypeptidase precursor Cytoplasmic (ec 3.4.17.—) M16 (pitrilysin family) RXF03441.1 Coenzyme pqq synthesis protein F Non-secretory (ec 3.4.99.—) RXF01918.1 zinc protease (ec 3.4.99.—) Signal peptide RXF01919.1 zinc protease (ec 3.4.99.—) Periplasmic RXF03699.2 processing peptidase (ec 3.4.24.64) Signal peptide M17 (leucyl aminopeptidase RXF00285.2 Cytosol aminopeptidase (ec Non-secretory family) 3.4.11.1) M18 RXF07879.1 Aspartyl aminopeptidase (ec Cytoplasmic 3.4.11.21) M20 RXF00811.1 dapE Succinyl-diaminopimelate Cytoplasmic desuccinylase (ec 3.5.1.18) RXF04052.2 Xaa-His dipeptidase (ec 3.4.13.3) Signal peptide RXF01822.2 Carboxypeptidase G2 precursor (ec Signal peptide 3.4.17.11) RXF09831.2:: N-acyl-L-amino acid Signal peptide RXF04892.1 amidohydrolase (ec 3.5.1.14) M28 (aminopeptidase Y family) RXF03488.2 Alkaline phosphatase isozyme OuterMembrane conversion protein precursor (ec 3.4.11.—) M42 (glutamyl aminopeptidase RXF05615.1 Deblocking aminopeptidase (ec Non-secretory family) 3.4.11.—) M22 RXF05817.1 O-sialoglycoprotein endopeptidase Extracellular (ec 3.4.24.57) RXF03065.2 Glycoprotease protein family Non-secretory M23 RXF01291.2 Cell wall endopeptidase, family Signal peptide M23/M37 RXF03916.1 Membrane proteins related to Signal peptide metalloendopeptidases RXF09147.2 Cell wall endopeptidase, family Signal peptide M23/M37 M24 RXF04693.1 Methionine aminopeptidase (ec Cytoplasmic 3.4.11.18) RXF03364.1 Methionine aminopeptidase (ec Non-secretory 3.4.11.18) RXF02980.1 Xaa-Pro aminopeptidase (ec Cytoplasmic 3.4.11.9) RXF06564.1 Xaa-Pro aminopeptidase (ec Cytoplasmic 3.4.11.9) M48 (Ste24 endopeptidase family) RXF05137.1 Heat shock protein HtpX Cytoplasmic Membrane RXF05081.1 Zinc metalloprotease (ec 3.4.24.—) Signal peptide M50 (S2P protease family) RXF04692.1 Membrane metalloprotease Cytoplasmic Membrane Serine Peptidases S1 (chymotrypsin family) RXF01250.2 protease do (ec 3.4.21.—) Periplasmic RXF07210.1 protease do (ec 3.4.21.—) Periplasmic S8 (subtilisin family) RXF06755.2 serine protease (ec 3.4.21.—) Non-secretory RXF08517.1 serine protease (ec 3.4.21.—) Extracellular RXF08627.2 extracellular serine protease (ec Signal peptide 3.4.21.—) RXF06281.1 Extracellular serine protease Non-secretory precursor (ec 3.4.21.—) RXF08978.1 extracellular serine protease (ec OuterMembrane 3.4.21.—) RXF06451.1 serine protease (ec 3.4.21.—) Signal peptide S9 (prolyl oligopeptidase family) RXF02003.2 Protease ii (ec 3.4.21.83) Periplasmic RXF00458.2 Hydrolase Non-secretory S11 (D-Ala-D-Ala carboxypeptidase RXF04657.2 D-alanyl-D-alanine-endopeptidase Periplasmic A family) (ec 3.4.99.—) RXF00670.1 D-alanyl-D-alanine Cytoplasmic carboxypeptidase (ec 3.4.16.4) Membrane S13 (D-Ala-D-Ala peptidase C RXF00133.1 D-alanyl-meso-diaminopimelate OuterMembrane family) endopeptidase (ec 3.4.—.—) RXF04960.2 D-alanyl-meso-diaminopimelate Signal peptide endopeptidase (ec 3.4.—.—) S14 (ClpP endopeptidase family) RXF04567.1 clpP atp-dependent Clp protease Non-secretory proteolytic subunit (ec 3.4.21.92) RXF04663.1 clpP atp-dependent Clp protease Cytoplasmic proteolytic subunit (ec 3.4.21.92) S16 (Ion protease family) RXF04653.2 atp-dependent protease La (ec Cytoplasmic 3.4.21.53) RXF08653.1 atp-dependent protease La (ec Cytoplasmic 3.4.21.53) RXF05943.1 atp-dependent protease La (ec Cytoplasmic 3.4.21.53) S24 (LexA family) RXF00449.1 LexA repressor (ec 3.4.21.88) Non-secretory RXF03397.1 LexA repressor (ec 3.4.21.88) Cytoplasmic S26 (signal peptidase I family) RXF01181.1 Signal peptidase I (ec 3.4.21.89) Cytoplasmic Membrane S33 RXF05236.1 pip3 Proline iminopeptidase (ec 3.4.11.5) Non-secretory RXF04802.1 pip1 Proline iminopeptidase (ec 3.4.11.5) Non-secretory RXF04808.2 pip2 Proline iminopeptidase (ec 3.4.11.5) Cytoplasmic S41 (C-terminal processing RXF06586.1 Tail-specific protease (ec 3.4.21.—) Signal peptide peptidase family) RXF01037.1 Tail-specific protease (ec 3.4.21.—) Signal peptide S45 RXF07170.1 pacB Penicillin acylase (ec 3.5.1.11) Signal peptide 2 RXF06399.2 pacB Penicillin acylase ii (ec 3.5.1.11) Signal peptide 1 S49 (protease IV family) RXF06993.2 possible protease sohb (ec 3.4.—.—) Non-secretory RXF01418.1 protease iv (ec 3.4.—.—) Non-secretory S58 (DmpA aminopeptidase family) RXF06308.2 D-aminopeptidase (ec 3.4.11.19) Cytoplasmic Membrane Threonine Peptidases T1 (proteasome family) RXF01961.2 hslV atp-dependent protease hslV (ec Cytoplasmic 3.4.25.—) T3 (gamma-glutamyltransferase RXF02342.1 ggt1 Gamma-glutamyltranspeptidase (ec Periplasmic family) 2.3.2.2) RXF04424.2 ggt2 Gamma-glutamyltranspeptidase (ec Periplasmic 2.3.2.2) Unclassified Peptidases U32 RXF00428.1 protease (ec 3.4.—.—) Cytoplasmic RXF02151.2 protease (ec 3.4.—.—) Cytoplasmic U61 RXF04715.1 Muramoyltetrapeptide Non-secretory carboxypeptidase (ec 3.4.17.13) U62 RXF04971.2 pmbA PmbA protein Cytoplasmic RXF04968.2 TldD protein Cytoplasmic Non MEROPS Proteases RXF00325.1 Repressor protein C2 Non-secretory RXF02689.2 Microsomal dipeptidase (ec Cytoplasmic 3.4.13.19) RXF02739.1 membrane dipeptidase (3.4.13.19) Signal peptide RXF03329.2 Hypothetical Cytosolic Protein Cytoplasmic RXF02492.1 Xaa-Pro dipeptidase (ec 3.4.13.9) Cytoplasmic RXF04047.2 caax amino terminal protease Cytoplasmic family Membrane RXF08136.2 protease (transglutaminase-like Cytoplasmic protein) RXF09487.1 Zinc metalloprotease (ec 3.4.24.—) Non-secretory

Additional Protein Modification Enzymes

In another embodiment, the target gene comprises a gene involved in proper protein processing and/or modification. Common modifications include disulfide bond formation, glycosylation, acetylation, acylation, phosphorylation, and gamma-carboxylation, all of which can regulate protein folding and biological activity. A non-exhaustive list of several classes of enzymes involved in protein processing is found in Table 3. One of skill in the art will recognize how to identify a target gene useful in the host cell chosen for the array, or useful with the heterologous protein of interest, from among the classes of protein modification enzymes listed in Table 3. The target gene may be endogenous to the host cell utilized, may be endogenous to the organism from which the heterologous protein of interest is derived, or may be known to facilitate proper processing of a heterologously expressed protein of interest. It is also recognized that any gene involved in protein production can be targeted according to desired specifications for the heterologous protein of interest.

In embodiments, a target gene is a tmRNA tag-coding region. tmRNAs can add tags to proteins to target for degradation by a process called trans-translation as described, e.g. by Dulebohn, D., 2007 “Trans-Translation: The tmRNA-Mediated Surveillance Mechanism for Ribosome Rescue, Directed Protein Degradation, and Nonstop mRNA Decay”, incorporated herein by reference. An exemplary tmRNA sequence is provided as XFRNA203 (SEQ ID NO:157). The sequence of the molecule is shown below, with the tag coding sequence underlined and the TAA stop codon in bold. Deletion or mutation of tmRNA sequences can result in improved heterologous protein yield.

5′-GGGGCCGTTTAGGATTCGACGCCGGTCGCGAAACTTTAGGTGCATGC CGAGTTGGTAACAGAACTCGTAAATCCACTGTTGCAACTTCTTATAGTTG CCAATGACGAAAACTACGGCCAGGAATTCGCTCTCGCTGCG TAAGCAGCC TTAGCCCTGAGCTTCTGGTACCTTCGGGTCCAGCAATCACCAGGGGATGT CTGTAAACCCAAAGTGATTGTCATATAGAACAGAATCGCCGTGCAGTACG TTGTGGACGAAGCGGCTAAAACTTACACAACTCGCCCAAAGCACCCTGCC CTTCGGGTCGCTGAGGGTTAACTTAATAGAAACGGCTACGCATGTAGTAC CGACAGCGGAGTACTGGCGGACGGGGGTTCAAATCCCCCCGGCTCCACCA C-3′

TABLE 3 Classes of enzymes involved in protein processing Class Examples Glycosyltransferases (EC 2.4.1.18) α-glucan-branching glycosyltransferase enzymatic branching factor branching glycosyltransferase enzyme Q glucosan transglycosylase glycogen branching enzyme amylose isomerase plant branching enzyme α-1,4-glucan:α-1,4-glucan-6-glycosyltransferase starch branching enzyme UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase GDP-fucose protein O-fucosyltransferase 2 O-GlcNAc transferase Histone acetyltransferase (EC 2.3.1.48) nucleosome-histone acetyltransferase histone acetokinase histone acetylase histone transacetylase histone deacetylase Protein kinase (EC 2.7) non-specific serine/threonine protein kinase Fas-activated serine/threonine kinase Goodpasture antigen-binding protein kinase IκB kinase cAMP-dependent protein kinase cGMP-dependent protein kinase protein kinase C polo kinase cyclin-dependent kinase mitogen-activated protein kinase mitogen-activated protein kinase kinase kinase receptor protein serine/threonine kinase dual-specificity kinase Phosphatase (EC 3.1.3.48) protein-tyrosine-phosphatase phosphotyrosine phosphatase phosphoprotein phosphatase (phosphotyrosine) phosphotyrosine histone phosphatase protein phosphotyrosine phosphatase tyrosylprotein phosphatase phosphotyrosine protein phosphatase phosphotyrosylprotein phosphatase tyrosine O-phosphate phosphatase PPT-phosphatase PTPase [phosphotyrosine]protein phosphatase PTP-phosphatase Methods for Modulating the Expression of Target Genes

One or more host cell populations of the array can be modified by any technique known in the art, for example by a technique wherein at least one target gene is knocked out of the genome, or by mutating at least one target gene to reduce expression of the gene, by altering at least one promoter of at least one target gene to reduce expression of the target gene, or by coexpressing (with the heterologous protein or polypeptide of interest) the target gene or an inhibitor of the target gene in the host genome. As discussed supra, the target gene can be endogenous to the host cell populations in the array, or can be heterologously expressed in each of the host cell populations.

The expression of target genes can be increased, for example, by introducing into at least one cell in a host population an expression vector comprising one or more target genes involved in protein production. The target gene expression can also be increased, for example, by mutating a promoter of a target gene. A host cell or organism that expresses a heterologous protein can also be genetically modified to increase the expression of at least one target gene involved in protein production and decrease the expression of at least one target gene involved in protein degradation.

The genome may be modified to modulate the expression of one or more target genes by including an exogenous gene or promoter element in the genome or in the host with an expression vector, by enhancing the capacity of a particular target gene to produce mRNA or protein, by deleting or disrupting a target gene or promoter element, or by reducing the capacity of a target gene to produce mRNA or protein. The genetic code can be altered, thereby affecting transcription and/or translation of a target gene, for example through substitution, deletion (“knock-out”), co-expression, or insertion (“knock-in”) techniques. Additional genes for a desired protein or regulatory sequence that modulate transcription of an existing target sequence can also be inserted.

Genome Modification

The genome of the host cell can be modified via a genetic targeting event, which can be by insertion or recombination, for example homologous recombination. Homologous recombination refers to the process of DNA recombination based on sequence homology. Homologous recombination permits site-specific modifications in endogenous genes and thus novel alterations can be engineered into a genome (see, for example Radding (1982) Ann. Rev. Genet. 16: 405; U.S. Pat. No. 4,888,274).

Various constructs can be prepared for homologous recombination at a target locus. Usually, the construct can include at least 10 bp, 20 bp, 30 bp, 40 bp, 50 bp, 70 bp, 100 bp, 500 bp, 1 kbp, 2 kbp, 4 kbp, 5 kbp, 10 kbp, 15 kbp, 20 kbp, or 50 kbp of sequence homologous with the identified locus. Various considerations can be involved in determining the extent of homology of target gene sequences, such as, for example, the size of the target locus, availability of sequences, relative efficiency of double cross-over events at the target locus and the similarity of the target sequence with other sequences.

The modified gene can include a sequence in which DNA substantially isogenic flanks the desired sequence modifications with a corresponding target sequence in the genome to be modified. The “modified gene” is the sequence being introduced into the genome to alter the expression of a protease or a protein folding modulator in the host cell. The “target gene” is the sequence that is being replaced by the modified gene. The substantially isogenic sequence can be at least about 95%, 97-98%, 99.0-99.5%, 99.6-99.9%, or 100% identical to the corresponding target sequence (except for the desired sequence modifications). The modified gene and the targeted gene can share stretches of DNA at least about 10, 20, 30, 50, 75, 150 or 500 base pairs that are 100% identical.

Nucleotide constructs can be designed to modify the endogenous, target gene product. The modified gene sequence can have one or more deletions, insertions, substitutions or combinations thereof designed to disrupt the function of the resultant gene product. In one embodiment, the alteration can be the insertion of a selectable marker gene fused in reading frame with the upstream sequence of the target gene.

The genome can also be modified using insertional inactivation. In this embodiment, the genome is modified by recombining a sequence in the gene that inhibits gene product formation. This insertion can either disrupt the gene by inserting a separate element, or remove an essential portion of the gene. In one embodiment, the insertional deletion also includes insertion of a gene coding for resistance to a particular stressor, such as an antibiotic, or for growth in a particular media, for example for production of an essential amino acid.

The genome can also be modified by use of transposons, which are genetic elements capable of inserting at sites in prokaryote genomes by mechanisms independent of homologous recombination. Transposons can include, for example, Tn7, Tn5, or Tn10 in E. coli, Tn554 in S. aureus, IS900 in M. paratuberculosis, IS492 from Pseudomonas atlantica, IS116 from Streptomyces and IS900 from M. paratuberculosis. Steps believed to be involved in transposition include cleavage of the end of the transposon to yield 3′OH; strand transfer, in which transposase brings together the 3′OH exposed end of transposon and the identified sequence; and a single step transesterification reaction to yield a covalent linkage of the transposon to the identified DNA. The key reaction performed by transposase is generally thought to be nicking or strand exchange, the rest of the process is done by host enzymes.

In one embodiment, the expression or activity of a target gene or protein is increased by incorporating a genetic sequence encoding the target protein or homolog thereof into the genome by recombination. In another embodiment, a promoter is inserted into the genome to enhance the expression of the target gene or homolog. In another embodiment, the expression or activity of a target gene or homolog thereof is decreased by recombination with an inactive gene. In another embodiment, a sequence that encodes a different gene, which can have a separate function in the cell or can be a reporter gene such as a resistance marker or an otherwise detectable marker gene, can be inserted into the genome through recombination. In yet another embodiment, a copy of at least a portion of the target gene that has been mutated at one or more locations is inserted into the genome through recombination. The mutated version of the target gene may not encode a protein, or the protein encoded by the mutated gene may be rendered inactive, the activity may be modulated (either increased or decreased), or the mutant protein can have a different activity when compared to the native protein.

There are strategies to knock out genes in bacteria, which have been generally exemplified in E. coli. One route is to clone a gene-internal DNA fragment into a vector containing an antibiotic resistance gene (e.g. ampicillin). Before cells are transformed via conjugative transfer, chemical transformation or electroporation (Puehler, et al. (1984) Advanced Molecular Genetics New York, Heidelberg, Berlin, Tokyo, Springer Verlag), an origin of replication, such as the vegetative plasmid replication (the oriV locus) is excised and the remaining DNA fragment is re-ligated and purified (Sambrook, et al. (2000) Molecular cloning: A laboratory manual, third edition Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory Press). Alternatively, antibiotic-resistant plasmids that have a DNA replication origin can be used. After transformation, the cells are plated onto e.g. LB agar plates containing the appropriate antibiotics (e.g. 200 micrograms/mL ampicillin). Colonies that grow on the plates containing the antibiotics presumably have undergone a single recombination event (Snyder, L., W. Champness, et al. (1997) Molecular Genetics of Bacteria Washington D.C., ASM Press) that leads to the integration of the entire DNA fragment into the genome at the homologous locus. Further analysis of the antibiotic-resistant cells to verify that the desired gene knock-out has occurred at the desired locus is e.g. by diagnostic PCR (McPherson, M. J., P. Quirke, et al. (1991) PCR: A Practical Approach New York, Oxford University Press). Here, at least two PCR primers are designed: one that hybridizes outside the DNA region that was used for the construction of the gene knock-out; and one that hybridizes within the remaining plasmid backbone. Successful PCR amplification of the DNA fragment with the correct size followed by DNA sequence analysis will verify that the gene knock-out has occurred at the correct location in the bacterial chromosome. The phenotype of the newly constructed mutant strain can then be analyzed by, e.g., SDS polyacrylamide gel electrophoresis (Simpson, R. J. (2003) Proteins and Proteomics—A Laboratory Manual. Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory Press).

An alternate route to generate a gene knock-out is by use of a temperature-sensitive replicon, such as the pSC101 replicon to facilitate gene replacement (Hamilton, et al. (1989) Journal of Bacteriology 171(9): 4617-22). The process proceeds by homologous recombination between a gene on a chromosome and homologous sequences carried on a plasmid temperature sensitive for DNA replication. After transformation of the plasmid into the appropriate host, it is possible to select for integration of the plasmid into the chromosome at 44° C. Subsequent growth of these cointegrates at 30° C. leads to a second recombination event, resulting in their resolution. Depending on where the second recombination event takes place, the chromosome will either have undergone a gene replacement or retain the original copy of the gene.

Other strategies have been developed to inhibit expression of particular gene products. For example, RNA interference (RNAi), particularly using small interfering RNA (siRNA), has been extensively developed to reduce or even eliminate expression of a particular gene product. siRNAs are short, double-stranded RNA molecules that can target complementary mRNAs for degradation. RNAi is the phenomenon in which introduction of a double-stranded RNA suppresses the expression of the homologous gene. dsRNA molecules are reduced in vivo to 21-23 nt siRNAs which are the mediators of the RNAi effect. Upon introduction, double stranded RNAs get processed into 20-25 nucleotide siRNAs by an RNase III-like enzyme called Dicer (initiation step). Then, the siRNAs assemble into endoribonuclease-containing complexes known as RNA-induced silencing complexes (RISCs), unwinding in the process. The siRNA strands subsequently guide the RISCs to complementary RNA molecules, where they cleave and destroy the cognate RNA (effecter step). Cleavage of cognate RNA takes place near the middle of the region bound by the siRNA strand. RNAi has been successfully used to reduce gene expression in a variety of organisms including zebrafish, nematodes (C. elegans), insects (Drosophila melanogaster), planaria, cnidaria, trypanosomes, mice and mammalian cells.

The genome can also be modified by mutation of one or more nucleotides in an open reading frame encoding a target gene. Techniques for genetic mutation, for instance site directed mutagenesis, are well known in the art. Some approaches focus on the generation of random mutations in chromosomal DNA such as those induced by X-rays and chemicals.

Coexpression

In one embodiment, one or more target genes in the host cell can be modified by including one or more vectors that encode the target gene(s) to facilitate coexpression of the target gene with the heterologous protein or peptide. In another embodiment, the host cell is modified by enhancing a promoter for a target gene, including by adding an exogenous promoter to the host cell genome.

In another embodiment, one or more target genes in the host cell is modified by including one or more vectors that encode an inhibitor of a target gene, such as a protease inhibitor to inhibit the activity of a target protease. Such an inhibitor can be an antisense molecule that limits the expression of the target gene, a cofactor of the target gene or a homolog of the target gene. Antisense is generally used to refer to a nucleic acid molecule with a sequence complementary to at least a portion of the target gene. In addition, the inhibitor can be an interfering RNA or a gene that encodes an interfering RNA. In Eukaryotic organisms, such an interfering RNA can be a small interfering RNA or a ribozyme, as described, for example, in Fire, A. et al. (1998) Nature 391:806-11, Elbashir et al. (2001) Genes & Development 15(2):188-200, Elbashir et al. (2001) Nature 411(6836):494-8, U.S. Pat. No. 6,506,559 to Carnegie Institute, U.S. Pat. No. 6,573,099 to Benitec, U.S. patent application Nos. 2003/0108923 to the Whitehead Inst., and 2003/0114409, PCT Publication Nos. WO03/006477, WO03/012052, WO03/023015, WO03/056022, WO03/064621 and WO03/070966.

The inhibitor can also be another protein or peptide. The inhibitor can, for example, be a peptide with a consensus sequence for the target protein. The inhibitor can also be a protein or peptide that can produce a direct or indirect inhibitory molecule for the target protein in the host. For example, protease inhibitors can include Amastatin, E-64, Antipain, Elastatinal, APMSF, Leupeptin, Bestatin, Pepstatin, Benzamidine, 1,10-Phenanthroline, Chymostatin, Phosphoramidon, 3,4-dichloroisocoumarin, TLCK, DFP, TPCK. Over 100 naturally occurring protein protease inhibitors have been identified so far. They have been isolated in a variety of organisms from bacteria to animals and plants. They behave as tight-binding reversible or pseudo-irreversible inhibitors of proteases preventing substrate access to the active site through steric hindrance. Their size are also extremely variable from 50 residues (e.g BPTI: Bovine Pancreatic Trypsin Inhibitor) to up to 400 residues (e.g alpha-1PI: alpha-1 Proteinase Inhibitor). They are strictly class-specific except proteins of the alpha-macroglobulin family (e.g alpha-2 macroglobulin) which bind and inhibit most proteases through a molecular trap mechanism.

An exogenous vector or DNA construct can be transfected or transformed into the host cell. Techniques for transfecting and transforming eukaryotic and prokaryotic cells respectively with exogenous nucleic acids are well known in the art. These can include lipid vesicle mediated uptake, calcium phosphate mediated transfection (calcium phosphate/DNA co-precipitation), viral infection, particularly using modified viruses such as, for example, modified adenoviruses, microinjection and electroporation. For prokaryotic transformation, techniques can include heat shock mediated uptake, bacterial protoplast fusion with intact cells, microinjection and electroporation. Techniques for plant transformation include Agrobacterium mediated transfer, such as by A. tumefaciens, rapidly propelled tungsten or gold microprojectiles, electroporation, microinjection and polyethelyne glycol mediated uptake. The DNA can be single or double stranded, linear or circular, relaxed or supercoiled DNA. For various techniques for transfecting mammalian cells, see, for example, Keown et al. (1990) Processes in Enzymology Vol. 185, pp. 527-537.

An expression construct encoding a target gene or an enhancer or inhibitor thereof can be constructed as described below for the expression constructs comprising the heterologous protein or polypeptide of interest. For example, the constructs can contain one, or more than one, internal ribosome entry site (IRES). The construct can also contain a promoter operably linked to the nucleic acid sequence encoding at least a portion of the target gene, or a cofactor of the target gene, a mutant version of at least a portion of the target gene, or in some embodiments, an inhibitor of the target gene. Alternatively, the construct can be promoterless. In cases in which the construct is not designed to incorporate into the cellular DNA/genome, the vector typically contains at least one promoter element. In addition to the nucleic acid sequences, the expression vector can contain selectable marker sequences. The expression constructs can further contain sites for transcription initiation, termination, and/or ribosome binding sites. The identified constructs can be inserted into and can be expressed in any prokaryotic or eukaryotic cell, including, but not limited to bacterial cells, such as P. fluorescens or E. coli, yeast cells, mammalian cells, such as CHO cells, or plant cells.

The construct can be prepared in accordance with processes known in the art. Various fragments can be assembled, introduced into appropriate vectors, cloned, analyzed and then manipulated further until the desired construct has been achieved. Various modifications can be made to the sequence, to allow for restriction analysis, excision, identification of probes, etc. Silent mutations can be introduced, as desired. At various stages, restriction analysis, sequencing, amplification with the polymerase chain reaction, primer repair, in vitro mutagenesis, etc. can be employed. Processes for the incorporation of antibiotic resistance genes and negative selection factors will be familiar to those of ordinary skill in the art (see, e.g., WO 99/15650; U.S. Pat. No. 6,080,576; U.S. Pat. No. 6,136,566; Niwa, et al., J. Biochem. 113:343-349 (1993); and Yoshida, et al., Transgenic Research, 4:277-287 (1995)).

The construct can be prepared using a bacterial vector, including a prokaryotic replication system, e.g. an origin recognizable by a prokaryotic cell such as P. fluorescens or E. coli. A marker, the same as or different from the marker to be used for insertion, can be employed, which can be removed prior to introduction into the host cell. Once the vector containing the construct has been completed, it can be further manipulated, such as by deletion of certain sequences, linearization, or by introducing mutations, deletions or other sequences into the homologous sequence. In one embodiment, the target gene construct and the heterologous protein construct are part of the same expression vector, and may or may not be under the control of the same promoter element. In another embodiment, they are on separate expression vectors. After final manipulation, the construct can be introduced into the cell.

Cell Growth Conditions

The cell growth conditions for the host cells described herein include that which facilitates expression of the protein of interest in at least one strain in the array (or at least a proportion of cells thereof), and/or that which facilitates fermentation of the expressed protein of interest. As used herein, the term “fermentation” includes both embodiments in which literal fermentation is employed and embodiments in which other, non-fermentative culture modes are employed. Growth, maintenance, and/or fermentation of the populations of host cells in the array may be performed at any scale. However, where multiple populations of host cells are screened simultaneously, the scale will be limited by the number of different populations and the capacity to grow and test multiple populations of host cells. In one embodiment, the fermentation medium may be selected from among rich media, minimal media, and mineral salts media. In another embodiment either a minimal medium or a mineral salts medium is selected. In still another embodiment, a minimal medium is selected. In yet another embodiment, a mineral salts medium is selected.

Mineral salts media consists of mineral salts and a carbon source such as, e.g., glucose, sucrose, or glycerol. Examples of mineral salts media include, e.g., M9 medium, Pseudomonas medium (ATCC 179), Davis and Mingioli medium (see, B D Davis & E S Mingioli (1950) in J. Bact. 60:17-28). The mineral salts used to make mineral salts media include those selected from among, e.g., potassium phosphates, ammonium sulfate or chloride, magnesium sulfate or chloride, and trace minerals such as calcium chloride, borate, and sulfates of iron, copper, manganese, and zinc. No organic nitrogen source, such as peptone, tryptone, amino acids, or a yeast extract, is included in a mineral salts medium. Instead, an inorganic nitrogen source is used and this may be selected from among, e.g., ammonium salts, aqueous ammonia, and gaseous ammonia. A preferred mineral salts medium will contain glucose as the carbon source. In comparison to mineral salts media, minimal media can also contain mineral salts and a carbon source, but can be supplemented with, e.g., low levels of amino acids, vitamins, peptones, or other ingredients, though these are added at very minimal levels.

In one embodiment, media can be prepared using the components listed in Table 4 below. The components can be added in the following order: first (NH₄)HPO₄, KH₂PO₄ and citric acid can be dissolved in approximately 30 liters of distilled water; then a solution of trace elements can be added, followed by the addition of an antifoam agent, such as Ucolub N 115. Then, after heat sterilization (such as at approximately 121° C.), sterile solutions of glucose MgSO₄ and thiamine-HCL can be added. Control of pH at approximately 6.8 can be achieved using aqueous ammonia. Sterile distilled water can then be added to adjust the initial volume to 371 minus the glycerol stock (123 mL). The chemicals are commercially available from various suppliers, such as Merck.

TABLE 4 Medium composition Component Initial concentration KH₂PO₄ 13.3 g l⁻¹ (NH₄)₂HPO₄ 4.0 g l⁻¹ Citric Acid 1.7 g l⁻¹ MgSO₄—7H₂O 1.2 g l⁻¹ Trace metal solution 10 ml l⁻¹ Thiamin HCl 4.5 mg l⁻¹ Glucose-H₂O 27.3 g l⁻¹ Antifoam Ucolub N115 0.1 ml l⁻¹ Feeding solution MgSO₄—7H₂O 19.7 g l⁻¹ Glucose-H₂O 770 g l⁻¹ NH₃ 23 g Trace metal solution 6 g l⁻¹ Fe(III) citrate 1.5 g l⁻¹ MnCl₂—4H₂O 0.8 g l⁻¹ ZmCH₂COOI₂—2H₂O 0.3 g l⁻¹ H₃BO₃ 0.25 g l⁻¹ Na₂MoO₄—2H₂O 0.25 g l⁻¹ CoCl₂6H₂O 0.15 g l⁻¹ CuCl₂2H₂O 0.84 g l⁻¹ ethylene Dinitrilo-tetracetic acid Na₂ sah 2H₂O (Tritriplex III, Merck)

In the present invention, growth, culturing, and/or fermentation of the transformed host cells is performed within a temperature range permitting survival of the host cells, preferably a temperature within the range of about 4° C. to about 55° C., inclusive. Thus, e.g., the terms “growth” (and “grow,” “growing”), “culturing” (and “culture”), and “fermentation” (and “ferment,” “fermenting”), as used herein in regard to the host cells of the present invention, inherently means “growth,” “culturing,” and “fermentation,” within a temperature range of about 4° C. to about 55° C., inclusive. In addition, “growth” is used to indicate both biological states of active cell division and/or enlargement, as well as biological states in which a non-dividing and/or non-enlarging cell is being metabolically sustained, the latter use of the term “growth” being synonymous with the term “maintenance.”

The host cells of the array should be grown and maintained at a suitable temperature for normal growth of that cell type. Such normal growth temperatures may be readily selected based on the known growth requirements of the selected host cell. Preferably, during the establishment of the culture and particularly during course of the screening, the cell culture is incubated in a controlled CO₂/N₂ humidity suitable for growth of the selected cells before and after transformation with the heterologous protein or polypeptide of interest. The humidity of the incubation is controlled to minimize evaporation from the culture vessel, and permit the use of smaller volumes. Alternatively, or in addition to controlling humidity, the vessels may be covered with lids in order to minimize evaporation. Selection of the incubation temperature depends primarily upon the identity of the host cells utilized. Selection of the percent humidity to control evaporation is based upon the selected volume of the vessel and concentration and volume of the cell culture in the vessel, as well as upon the incubation temperature. Thus, the humidity may vary from about 10% to about 80%. It should be understood that selection of a suitable conditions is well within the skill of the art.

Screening

The strain array described herein can be screened for the optimal host cell population in which to express a heterologous protein of interest. The optimal host cell population can be identified or selected based on the quantity, quality, and/or location of the expressed protein of interest. In one embodiment, the optimal host cell population is one that results in an increased yield of the protein or polypeptide of interest within the host cell compared to other populations of phenotypically distinct host cells in the array, e.g., an indicator expression system.

An indicator expression system is any heterologous protein expression system that is used for comparison of protein expression. An indicator expression system can be a) a second test expression system present in the same array or b) a standard expression system. A second test expression system refers to any test expression system on the array that is different from the expression system on the array that is being compared to the indicator expression system. A standard expression system is a heterologous protein expression system used as a standard, for example, one comprising a host from which the test expression system for comparison was derived, the host transformed with a heterologous protein expression vector that does not contain a secretion leader. In other embodiments the vector is the same as that used in the test expression system. A standard expression system for use in a Pseudomonas expression array of the invention, can be, e.g., a DC454 expression system. A DC454 expression system refers to a DC454 host transformed with an expression vector encoding the heterologous protein. In other embodiments, the standard expression system contains expression elements (e.g., protease mutations, folding modulator overexpression constructs, secretion leaders) not present in a wild type expression system, but fewer or different expression elements than does the test expression system that is being compared. A standard expression system for use in an E. coli expression array of the invention can be, e.g., BL21(DE3), or any other appropriate strain selected by one of skill in the art for the experiment at hand. A null strain refers to a wild type host cell population transformed with a vector that does not express the heterologous protein.

The increased production alternatively can be an increased level of properly processed protein or polypeptide per gram of protein produced, or per gram of host protein. The increased production can also be an increased level of recoverable protein or polypeptide produced per gram of heterologous protein or per gram of host cell protein. The increased production can also be any combination of an increased level of total protein, increased level of properly processed or properly folded protein, or increased level of active or soluble protein. In this embodiment, the term “increased” or “improved” is relative to the level of protein or polypeptide that is produced, properly processed, soluble, and/or recoverable when the protein or polypeptide of interest is expressed in one or more other populations of host cells in the array. The increased production may optimize the efficiency of the cell or organism by for example, decreasing the energy expenditure, increasing the use of available resources, or decreasing the requirements for growth supplements in growth media. The increased production may also be the result of a decrease in proteolyic degradation of the expressed protein.

In one embodiment, at least one strain in the array produces at least 0.1 mg/ml correctly processed protein. A correctly processed protein has an amino terminus of the native protein. In another embodiment, at least one strain produces 0.1 to 10 mg/ml correctly processed protein in the cell, including at least about 0.2, about 0.3, about 0.4, about 0.5, about 0.6, about 0.7, about 0.8, about 0.9 or at least about 1.0 mg/ml correctly processed protein. In another embodiment, the total correctly processed protein or polypeptide of interest produced by at least one strain in the array is at least 1.0 mg/ml, at least about 2 mg/ml, at least about 3 mg/ml, about 4 mg/ml, about 5 mg/ml, about 6 mg/ml, about 7 mg/ml, about 8 mg/ml, about 10 mg/ml, about 15 mg/ml, about 20 mg/ml, about 25 mg/ml, about 30 mg/ml, about 35 mg/ml, about 40 mg/ml, about 45 mg/ml, at least about 50 mg/ml, or greater. In some embodiments, the amount of correctly processed protein produced is at least about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 96%, about 97%, about 98%, at least about 99%, or more of total heterologous protein in a correctly processed form.

An improved expression of a protein or polypeptide of interest can also refer to an increase in the solubility of the protein. The protein or polypeptide of interest can be produced and recovered from the cytoplasm, periplasm or extracellular medium of the host cell. The protein or polypeptide can be insoluble or soluble. The protein or polypeptide can include one or more targeting (e.g., signal or leader) sequences or sequences to assist purification, as discussed supra.

The term “soluble” as used herein means that the protein is not precipitated by centrifugation at between approximately 5,000 and 20,000× gravity when spun for 10-30 minutes in a buffer under physiological conditions. Soluble proteins are not part of an inclusion body or other precipitated mass. Similarly, “insoluble” means that the protein or polypeptide can be precipitated by centrifugation at between 5,000 and 20,000× gravity when spun for 10-30 minutes in a buffer under physiological conditions. Insoluble proteins or polypeptides can be part of an inclusion body or other precipitated mass. Some proteins, e.g., membrane proteins, can fractionate with the insoluble proteins, though they are active. Therefore, it is understood that an insoluble protein is not necessarily inactive. The term “inclusion body” is meant to include any intracellular body contained within a cell wherein an aggregate of proteins or polypeptides has been sequestered.

In another embodiment, the optimal host cell population produces an increased amount of the protein of interest that is transported to the periplasm or secreted into the extracellular space of the host cell. In one embodiment, at least one strain in the array produces at least 0.1 mg/ml protein in the periplasmic compartment. In another embodiment, at least one strain produces 0.1 to 10 mg/ml periplasmic protein in the cell, or at least about 0.2, about 0.3, about 0.4, about 0.5, about 0.6, about 0.7, about 0.8, about 0.9 or at least about 1.0 mg/ml periplasmic protein. In one embodiment, the total protein or polypeptide of interest produced by at least one strain in the array is at least 1.0 mg/ml, at least about 2 mg/ml, at least about 3 mg/ml, about 4 mg/ml, about 5 mg/ml, about 6 mg/ml, about 7 mg/ml, about 8 mg/ml, about 10 mg/ml, about 15 mg/ml, about 20 mg/ml, at least about 25 mg/ml, or greater. In some embodiments, the amount of periplasmic protein produced is at least about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99%, or more of total protein or polypeptide of interest produced.

At least one strain in the array of the invention can also lead to increased yield of the protein or polypeptide of interest. In one embodiment, at least one strain produces a protein or polypeptide of interest as at least about 5%, at least about 10%, about 15%, about 20%, about 25%, about 30%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, or greater of total cell protein (tcp). “Percent total cell protein” is the amount of protein or polypeptide in the host cell as a percentage of aggregate cellular protein. Methods for the determination of the percent total cell protein are well known in the art.

In a particular embodiment, at least one host cell population in the array can have a heterologous protein production level of at least 1% tcp and a cell density of at least 40 mg/ml, when grown (i.e. within a temperature range of about 4° C. to about 55° C., including about 10° C., about 15° C., about 20° C., about 25° C., about 30° C., about 35° C., about 40° C., about 45° C., and about 50° C.) in a mineral salts medium. In a particularly preferred embodiment, the expression system will have a protein or polypeptide expression level of at least 5% tcp and a cell density of at least 40 g/L, when grown (i.e. within a temperature range of about 4° C. to about 55° C., inclusive) in a mineral salts medium.

In practice, heterologous proteins targeted to the periplasm are often found in the broth (see European Patent No. EP 0 288 451), possibly because of damage to or an increase in the fluidity of the outer cell membrane. The rate of this “passive” secretion may be increased by using a variety of mechanisms that permeabilize the outer cell membrane, including: colicin (Miksch et al. (1997) Arch. Microbiol. 167: 143-150); growth rate (Shokri et al. (2002) App Miocrobiol Biotechnol 58:386-392); TolIII overexpression (Wan and Baneyx (1998) Protein Expression Purif. 14: 13-22); bacteriocin release protein (Hsiung et al. (1989) Bio/Technology 7: 267-71), colicin A lysis protein (Lloubes et al. (1993) Biochimie 75: 451-8) mutants that leak periplasmic proteins (Furlong and Sundstrom (1989) Developments in Indus. Microbio. 30: 141-8); fusion partners (Jeong and Lee (2002) Appl. Environ. Microbio. 68: 4979-4985); or, recovery by osmotic shock (Taguchi et al. (1990) Biochimica Biophysica Acta 1049: 278-85). Transport of engineered proteins to the periplasmic space with subsequent localization in the broth has been used to produce properly folded and active proteins in E. coli (Wan and Baneyx (1998) Protein Expression Purif. 14: 13-22; Simmons et al. (2002) J. Immun. Meth. 263: 133-147; Lundell et al. (1990) J. Indust. Microbio. 5: 215-27).

The method may also include the step of purifying the protein or polypeptide of interest from the periplasm or from extracellular media. The heterologous protein or polypeptide can be expressed in a manner in which it is linked to a tag protein and the “tagged” protein can be purified from the cell or extracellular media.

In some embodiments, the protein or polypeptide of interest can also be produced by at least one strain in the array in an active form. The term “active” means the presence of biological activity, wherein the biological activity is comparable or substantially corresponds to the biological activity of a corresponding native protein or polypeptide. In the context of proteins this typically means that a polynucleotide or polypeptide comprises a biological function or effect that has at least about 20%, about 50%, preferably at least about 60-80%, and most preferably at least about 90-95% activity compared to the corresponding native protein or polypeptide using standard parameters. However, in some embodiments, it may be desirable to produce a polypeptide that has altered or improved activity compared to the native protein (e.g, one that has altered or improved immunoreactivity, substrate specificity, etc). An altered or improved polypeptide may result from a particular conformation created by one or more of the host cell populations of the array.

The determination of protein or polypeptide activity can be performed utilizing corresponding standard, targeted comparative biological assays for particular proteins or polypeptides which can be used to assess biological activity.

The recovery of active protein or polypeptide of interest may also be improved in the optimal host strain compared to one or more other strains in the array of the invention. Active proteins can have a specific activity of at least about 20%, at least about 30%, at least about 40%, about 50%, about 60%, at least about 70%, about 80%, about 90%, or at least about 95% that of the native protein or polypeptide from which the sequence is derived. Further, the substrate specificity (k_(cat)/K_(m)) is optionally substantially similar to the native protein or polypeptide. Typically, k_(cat)/K_(m) will be at least about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, at least about 90%, at least about 95%, or greater. Methods of assaying and quantifying measures of protein and polypeptide activity and substrate specificity (k_(cat)/K_(m)), are well known to those of skill in the art.

Measurement of Protein Activity

The activity of the heterologously-expressed protein or polypeptide of interest can be compared with a previously established native protein or polypeptide standard activity. Alternatively, the activity of the protein or polypeptide of interest can be determined in a simultaneous, or substantially simultaneous, comparative assay with the native protein or polypeptide. For example, in vitro assays can be used to determine any detectable interaction between a protein or polypeptide of interest and a target, e.g. between an expressed enzyme and substrate, between expressed hormone and hormone receptor, between expressed antibody and antigen, etc. Such detection can include the measurement of calorimetric changes, proliferation changes, cell death, cell repelling, changes in radioactivity, changes in solubility, changes in molecular weight as measured by gel electrophoresis and/or gel exclusion methods, phosphorylation abilities, antibody specificity assays such as ELISA assays, etc. In addition, in vivo assays include, but are not limited to, assays to detect physiological effects of the heterologously expressed protein or polypeptide in comparison to physiological effects of the native protein or polypeptide, e.g. weight gain, change in electrolyte balance, change in blood clotting time, changes in clot dissolution and the induction of antigenic response. Generally, any in vitro or in vivo assay can be used to determine the active nature of the protein or polypeptide of interest that allows for a comparative analysis to the native protein or polypeptide so long as such activity is assayable. Alternatively, the proteins or polypeptides produced in at least one strain in the array of the present invention can be assayed for the ability to stimulate or inhibit interaction between the protein or polypeptide and a molecule that normally interacts with the protein or polypeptide, e.g. a substrate or a component of a signal pathway with which the native protein normally interacts. Such assays can typically include the steps of combining the protein with a substrate molecule under conditions that allow the protein or polypeptide to interact with the target molecule, and detect the biochemical consequence of the interaction with the protein and the target molecule.

Assays that can be utilized to determine protein or polypeptide activity are described, for example, in Ralph, P. J., et al. (1984) J. Immunol. 132:1858 or Saiki et al. (1981) J. Immunol. 127:1044, Steward, W. E. II (1980) The Interferon Systems. Springer-Verlag, Vienna and New York, Broxmeyer, H. E., et al. (1982) Blood 60:595, Molecular Cloning: A Laboratory Manual”, 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, J., E. F. Fritsch and T. Maniatis eds., 1989, and Methods in Enzymology: Guide to Molecular Cloning Techniques, Academic Press, Berger, S. L. and A. R. Kimmel eds., 1987, A K Patra et al., Protein Expr Purif, 18(2): p/182-92 (2000), Kodama et al., J. Biochem. 99: 1465-1472 (1986); Stewart et al., Proc. Nat'l Acad. Sci. USA 90: 5209-5213 (1993); (Lombillo et al., J. Cell Biol. 128:107-115 (1995); (Vale et al., Cell 42:39-50 (1985). Activity can be compared between samples of heterologously expressed protein derived from one or more of the other host cell populations in the array, or can be compared to the activity of a native protein, or both. Activity measurements can be performed on isolated protein, or can be performed in vitro in the host cell.

In another embodiment, protein production and/or activity may be monitored directly in the culture by fluorescence or spectroscopic measurements on, for example, a conventional microscope, luminometer, or plate reader. Where the protein of interest is an enzyme whose substrate is known, the substrate can be added to the culture media wherein a fluorescent signal is emitted when the substrate is converted by the enzyme into a product. In one embodiment, the expression construct encoding the heterologous protein or polypeptide of interest further encodes a reported protein. By “reporter protein” is meant a protein that by its presence in or on a cell or when secreted in the media allows the cell to be distinguished from a cell that does not contain the reporter protein. Production of the heterologous protein of interest results in a detectable change in the host cell population. The reporter molecule can be firefly luciferase and GFP or any other fluorescence molecule, as well as beta-galactosidase gene (beta.gal) and chloramphenicol and acetyltransferase gene (CAT). Assays for expression produced in conjunction with each of these reporter gene elements are well-known to those skilled in the art.

The reporter gene can encode a detectable protein or an indirectly detectable protein, or the reporter gene can be a survival gene. In a preferred embodiment, the reporter protein is a detectable protein. A “detectable protein” or “detection protein” (encoded by a detectable or detection gene) is a protein that can be used as a direct label; that is, the protein is detectable (and preferably, a cell comprising the detectable protein is detectable) without further manipulation. Thus, in this embodiment, the protein product of the reporter gene itself can serve to distinguish cells that are expressing the detectable gene. In this embodiment, suitable detectable genes include those encoding autofluorescent proteins.

As is known in the art, there are a variety of autofluorescent proteins known; these generally are based on the green fluorescent protein (GFP) from Aequorea and variants thereof; including, but not limited to, GFP, (Chalfie, et al. (1994) Science 263(5148):802-805); enhanced GFP (EGFP; Clontech—Genbank Accession Number U55762)), blue fluorescent protein (BFP; Quantum Biotechnologies, Inc., Montreal, Canada); Stauber (1998) Biotechniques 24(3):462-471; Heim and Tsien (1996) Curr. Biol. 6:178-182), enhanced yellow fluorescent protein (EYFP; Clontech Laboratories, Inc., Palo Alto, Calif.) and red fluorescent protein. In addition, there are recent reports of autofluorescent proteins from Renilla and Ptilosarcus species. See WO 92/15673; WO 95/07463; WO 98/14605; WO 98/26277; WO 99/49019; U.S. Pat. No. 5,292,658; U.S. Pat. No. 5,418,155; U.S. Pat. No. 5,683,888; U.S. Pat. No. 5,741,668; U.S. Pat. No. 5,777,079; U.S. Pat. No. 5,804,387; U.S. Pat. No. 5,874,304; U.S. Pat. No. 5,876,995; and U.S. Pat. No. 5,925,558; all of which are expressly incorporated herein by reference.

Isolation of Protein or Polypeptide of Interest

To measure the yield, solubility, conformation, and/or activity of the protein of interest, it may be desirable to isolate the protein from one or more strains in the array. The isolation may be a crude, semi-crude, or pure isolation, depending on the requirements of the assay used to make the appropriate measurements. The protein may be produced in the cytoplasm, targeted to the periplasm, or may be secreted into the culture or fermentation media. To release proteins targeted to the periplasm, treatments involving chemicals such as chloroform (Ames et al. (1984) J. Bacteriol., 160: 1181-1183), guanidine-HCl, and Triton X-100 (Naglak and Wang (1990) Enzyme Microb. Technol., 12: 603-611) have been used. However, these chemicals are not inert and may have detrimental effects on many heterologous protein products or subsequent purification procedures. Glycine treatment of E. coli cells, causing permeabilization of the outer membrane, has also been reported to release the periplasmic contents (Ariga et al. (1989) J. Ferm. Bioeng., 68: 243-246). The most widely used methods of periplasmic release of heterologous protein are osmotic shock (Nosal and Heppel (1966) J. Biol. Chem., 241: 3055-3062; Neu and Heppel (1965) J. Biol. Chem., 240: 3685-3692), hen Egg white (HEW)-lysozyme/ethylenediamine tetraacetic acid (EDTA) treatment (Neu and Heppel (1964) J. Biol. Chem., 239: 3893-3900; Witholt et al. (1976) Biochim. Biophys. Acta, 443: 534-544; Pierce et al. (1995) ICheme Research. Event, 2: 995-997), and combined HEW-lysozyme/osmotic shock treatment (French et al. (1996) Enzyme and Microb. Tech., 19: 332-338). The French method involves resuspension of the cells in a fractionation buffer followed by recovery of the periplasmic fraction, where osmotic shock immediately follows lysozyme treatment.

Typically, these procedures include an initial disruption in osmotically-stabilizing medium followed by selective release in non-stabilizing medium. The composition of these media (pH, protective agent) and the disruption methods used (chloroform, HEW-lysozyme, EDTA, sonication) vary among specific procedures reported. A variation on the HEW-lysozyme/EDTA treatment using a dipolar ionic detergent in place of EDTA is discussed by Stabel et al. (1994) Veterinary Microbiol., 38: 307-314. For a general review of use of intracellular lytic enzyme systems to disrupt E. coli, see Dabora and Cooney (1990) in Advances in Biochemical Engineering/Biotechnology, Vol. 43, A. Fiechter, ed. (Springer-Verlag: Berlin), pp. 11-30.

Conventional methods for the recovery of proteins or polypeptides of interest from the cytoplasm, as soluble protein or refractile particles, involved disintegration of the bacterial cell by mechanical breakage. Mechanical disruption typically involves the generation of local cavitation in a liquid suspension, rapid agitation with rigid beads, sonication, or grinding of cell suspension (Bacterial Cell Surface Techniques, Hancock and Poxton (John Wiley & Sons Ltd, 1988), Chapter 3, p. 55).

HEW-lysozyme acts biochemically to hydrolyze the peptidoglycan backbone of the cell wall. The method was first developed by Zinder and Arndt (1956) Proc. Natl. Acad. Sci. USA, 42: 586-590, who treated E. coli with egg albumin (which contains HEW-lysozyme) to produce rounded cellular spheres later known as spheroplasts. These structures retained some cell-wall components but had large surface areas in which the cytoplasmic membrane was exposed. U.S. Pat. No. 5,169,772 discloses a method for purifying heparinase from bacteria comprising disrupting the envelope of the bacteria in an osmotically-stabilized medium, e.g., 20% sucrose solution using, e.g., EDTA, lysozyme, or an organic compound, releasing the non-heparinase-like proteins from the periplasmic space of the disrupted bacteria by exposing the bacteria to a low-ionic-strength buffer, and releasing the heparinase-like proteins by exposing the low-ionic-strength-washed bacteria to a buffered salt solution.

Many different modifications of these methods have been used on a wide range of expression systems with varying degrees of success (Joseph-Liazun et al. (1990) Gene, 86: 291-295; Carter et al. (1992) Bio/Technology, 10: 163-167). Efforts to induce recombinant cell culture to produce lysozyme have been reported. EP 0 155 189 discloses a means for inducing a recombinant cell culture to produce lysozymes, which would ordinarily be expected to kill such host cells by means of destroying or lysing the cell wall structure.

U.S. Pat. No. 4,595,658 discloses a method for facilitating externalization of proteins transported to the periplasmic space of bacteria. This method allows selective isolation of proteins that locate in the periplasm without the need for lysozyme treatment, mechanical grinding, or osmotic shock treatment of cells. U.S. Pat. No. 4,637,980 discloses producing a bacterial product by transforming a temperature-sensitive lysogen with a DNA molecule that codes, directly or indirectly, for the product, culturing the transformant under permissive conditions to express the gene product intracellularly, and externalizing the product by raising the temperature to induce phage-encoded functions. Asami et al. (1997) J. Ferment. and Bioeng., 83: 511-516 discloses synchronized disruption of E. coli cells by T4 phage infection, and Tanji et al. (1998) J. Ferment. and Bioeng., 85: 74-78 discloses controlled expression of lysis genes encoded in T4 phage for the gentle disruption of E. coli cells.

Upon cell lysis, genomic DNA leaks out of the cytoplasm into the medium and results in significant increase in fluid viscosity that can impede the sedimentation of solids in a centrifugal field. In the absence of shear forces such as those exerted during mechanical disruption to break down the DNA polymers, the slower sedimentation rate of solids through viscous fluid results in poor separation of solids and liquid during centrifugation. Other than mechanical shear force, there exist nucleolytic enzymes that degrade DNA polymer. In E. coli, the endogenous gene endA encodes for an endonuclease (molecular weight of the mature protein is approx. 24.5 kD) that is normally secreted to the periplasm and cleaves DNA into oligodeoxyribonucleotides in an endonucleolytic manner. It has been suggested that endA is relatively weakly expressed by E. coli (Wackemagel et al. (1995) Gene 154: 55-59).

If desired, the proteins produced using one or more strains in the array of this invention may be isolated and purified to substantial purity by standard techniques well known in the art, including, but not limited to, ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, nickel chromatography, hydroxylapatite chromatography, reverse phase chromatography, lectin chromatography, preparative electrophoresis, detergent solubilization, selective precipitation with such substances as column chromatography, immunopurification methods, and others. For example, proteins having established molecular adhesion properties can be reversibly fused with a ligand. With the appropriate ligand, the protein can be selectively adsorbed to a purification column and then freed from the column in a relatively pure form. The fused protein is then removed by enzymatic activity. In addition, protein can be purified using immunoaffinity columns or Ni-NTA columns. General techniques are further described in, for example, R. Scopes, Protein Purification: Principles and Practice, Springer-Verlag: N.Y. (1982); Deutscher, Guide to Protein Purification, Academic Press (1990); U.S. Pat. No. 4,511,503; S. Roe, Protein Purification Techniques: A Practical Approach (Practical Approach Series), Oxford Press (2001); D. Bollag, et al., Protein Methods, Wiley-Lisa, Inc. (1996); A K Patra et al., Protein Expr Purif, 18(2): p/182-92 (2000); and R. Mukhija, et al., Gene 165(2): p. 303-6 (1995). See also, for example, Ausubel, et al. (1987 and periodic supplements); Deutscher (1990) “Guide to Protein Purification,” Methods in Enzymology vol. 182, and other volumes in this series; Coligan, et al. (1996 and periodic Supplements) Current Protocols in Protein Science Wiley/Greene, NY; and manufacturer's literature on use of protein purification products, e.g., Pharmacia, Piscataway, N.J., or Bio-Rad, Richmond, Calif. Combination with recombinant techniques allow fusion to appropriate segments, e.g., to a FLAG sequence or an equivalent which can be fused via a protease-removable sequence. See also, for example., Hochuli (1989) Chemische Industrie 12:69-70; Hochuli (1990) “Purification of Recombinant Proteins with Metal Chelate Absorbent” in Setlow (ed.) Genetic Engineering, Principle and Methods 12:87-98, Plenum Press, NY; and Crowe, et al. (1992) QIAexpress: The High Level Expression & Protein Purification System QUIAGEN, Inc., Chatsworth, Calif.

Detection of the expressed protein is achieved by methods known in the art and include, for example, radioimmunoassays, Western blotting techniques or immunoprecipitation.

Certain proteins expressed by the strains in the array of this invention may form insoluble aggregates (“inclusion bodies”). Several protocols are suitable for purification of proteins from inclusion bodies. For example, purification of inclusion bodies typically involves the extraction, separation and/or purification of inclusion bodies by disruption of the host cells, e.g., by incubation in a buffer of 50 mM TRIS/HCL pH 7.5, 50 mM NaCl, 5 mM MgCl₂, 1 mM DTT, 0.1 mM ATP, and 1 mM PMSF. The cell suspension is typically lysed using 2-3 passages through a French Press. The cell suspension can also be homogenized using a Polytron (Brinkman Instruments) or sonicated on ice. Alternate methods of lysing bacteria are apparent to those of skill in the art (see, e.g., Sambrook et al., supra; Ausubel et al., supra).

If necessary, the inclusion bodies can be solubilized, and the lysed cell suspension typically can be centrifuged to remove unwanted insoluble matter. Proteins that formed the inclusion bodies may be renatured by dilution or dialysis with a compatible buffer. Suitable solvents include, but are not limited to urea (from about 4 M to about 8 M), formamide (at least about 80%, volume/volume basis), and guanidine hydrochloride (from about 4 M to about 8 M). Although guanidine hydrochloride and similar agents are denaturants, this denaturation is not irreversible and renaturation may occur upon removal (by dialysis, for example) or dilution of the denaturant, allowing re-formation of immunologically and/or biologically active protein. Other suitable buffers are known to those skilled in the art.

The heterologously-expressed proteins present in the supernatant can be separated from the host proteins by standard separation techniques well known to those of skill in the art. For example, an initial salt fractionation can separate many of the unwanted host cell proteins (or proteins derived from the cell culture media) from the protein or polypeptide of interest. One such example can be ammonium sulfate. Ammonium sulfate precipitates proteins by effectively reducing the amount of water in the protein mixture. Proteins then precipitate on the basis of their solubility. The more hydrophobic a protein is, the more likely it is to precipitate at lower ammonium sulfate concentrations. A typical protocol includes adding saturated ammonium sulfate to a protein solution so that the resultant ammonium sulfate concentration is between 20-30%. This concentration will precipitate the most hydrophobic of proteins. The precipitate is then discarded (unless the protein of interest is hydrophobic) and ammonium sulfate is added to the supernatant to a concentration known to precipitate the protein of interest. The precipitate is then solubilized in buffer and the excess salt removed if necessary, either through dialysis or diafiltration. Other methods that rely on solubility of proteins, such as cold ethanol precipitation, are well known to those of skill in the art and can be used to fractionate complex protein mixtures.

The molecular weight of a protein or polypeptide of interest can be used to isolated it from proteins of greater and lesser size using ultrafiltration through membranes of different pore size (for example, Amicon or Millipore membranes). As a first step, the protein mixture can be ultrafiltered through a membrane with a pore size that has a lower molecular weight cut-off than the molecular weight of the protein of interest. The retentate of the ultrafiltration can then be ultrafiltered against a membrane with a molecular cut off greater than the molecular weight of the protein of interest. The protein or polypeptide of interest will pass through the membrane into the filtrate. The filtrate can then be chromatographed as described below.

The expressed proteins or polypeptides of interest can also be separated from other proteins on the basis of its size, net surface charge, hydrophobicity, and affinity for ligands. In addition, antibodies raised against proteins can be conjugated to column matrices and the proteins immunopurified. All of these methods are well known in the art. It will be apparent to one of skill that chromatographic techniques can be performed at any scale and using equipment from many different manufacturers (e.g., Pharmacia Biotech).

Renaturation and Refolding

Where heterologously expressed protein is produced in a denatured form, insoluble protein can be renatured or refolded to generate secondary and tertiary protein structure conformation. Protein refolding steps can be used, as necessary, in completing configuration of the heterologous product. Refolding and renaturation can be accomplished using an agent that is known in the art to promote dissociation/association of proteins. For example, the protein can be incubated with dithiothreitol followed by incubation with oxidized glutathione disodium salt followed by incubation with a buffer containing a refolding agent such as urea.

The protein or polypeptide of interest can also be renatured, for example, by dialyzing it against phosphate-buffered saline (PBS) or 50 mM Na-acetate, pH 6 buffer plus 200 mM NaCl. Alternatively, the protein can be refolded while immobilized on a column, such as the Ni NTA column by using a linear 6M-1M urea gradient in 500 mM NaCl, 20% glycerol, 20 mM Tris/HCl pH 7.4, containing protease inhibitors. The renaturation can be performed over a period of 1.5 hours or more. After renaturation the proteins can be eluted by the addition of 250 mM imidazole. Imidazole can be removed by a final dialyzing step against PBS or 50 mM sodium acetate pH 6 buffer plus 200 mM NaCl. The purified protein can be stored at 4° C. or frozen at −80° C.

Other methods include, for example, those that may be described in M H Lee et al., Protein Expr. Purif., 25(1): p. 166-73 (2002), W. K. Cho et al., J. Biotechnology, 77(2-3): p. 169-78 (2000), Ausubel, et al. (1987 and periodic supplements), Deutscher (1990) “Guide to Protein Purification,” Methods in Enzymology vol. 182, and other volumes in this series, Coligan, et al. (1996 and periodic Supplements) Current Protocols in Protein Science Wiley/Greene, NY, S. Roe, Protein Purification Techniques: A Practical Approach (Practical Approach Series), Oxford Press (2001); D. Bollag, et al., Protein Methods, Wiley-Lisa, Inc. (1996)

Expression Vectors

A heterologous protein of interest can be produced in one or more of the host cells disclosed herein by introducing into each strain an expression vector encoding the heterologous protein of interest. In one embodiment, the vector comprises a polynucleotide sequence encoding the protein of interest operably linked to a promoter capable of functioning in the chosen host cell, as well as all other required transcription and translation regulatory elements.

The term “operably linked” refers to any configuration in which the transcriptional and any translational regulatory elements are covalently attached to the encoding sequence in such disposition(s), relative to the coding sequence, that in and by action of the host cell, the regulatory elements can direct the expression of the coding sequence.

The heterologous protein of interest can be expressed from polynucleotides in which the heterologous polypeptide coding sequence is operably linked to transcription and translation regulatory elements to form a functional gene from which the host cell can express the protein or polypeptide. The coding sequence can be a native coding sequence for the heterologous polypeptide, or may be a coding sequence that has been selected, improved, or optimized for use in the selected expression host cell: for example, by synthesizing the gene to reflect the codon use bias of a host species. In one embodiment of the invention, the host species is a P. fluorescens, and the codon bias of P. fluorescens is taken into account when designing the polypeptide coding sequence. The gene(s) are constructed within or inserted into one or more vector(s), which can then be transformed into the expression host cell.

Other regulatory elements may be included in a vector (also termed “expression construct”). The vector will typically comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and to, if desirable, provide amplification within the host. Additional elements include, but are not limited to, for example, transcriptional enhancer sequences, translational enhancer sequences, other promoters, activators, translational start and stop signals, transcription terminators, cistronic regulators, polycistronic regulators, or tag sequences, such as nucleotide sequence “tags” and “tag” polypeptide coding sequences, which facilitates identification, separation, purification, and/or isolation of an expressed polypeptide.

In another embodiment, the expression vector further comprises a tag sequence adjacent to the coding sequence for the protein or polypeptide of interest. In one embodiment, this tag sequence allows for purification of the protein. The tag sequence can be an affinity tag, such as a hexa-histidine affinity tag (SEQ ID NO: 158). In another embodiment, the affinity tag can be a glutathione-5-transferase molecule. The tag can also be a fluorescent molecule, such as YFP or GFP, or analogs of such fluorescent proteins. The tag can also be a portion of an antibody molecule, or a known antigen or ligand for a known binding partner useful for purification.

A protein-encoding gene according to the present invention can include, in addition to the protein coding sequence, the following regulatory elements operably linked thereto: a promoter, a ribosome binding site (RBS), a transcription terminator, translational start and stop signals. Useful RBSs can be obtained from any of the species useful as host cells in expression systems according to the present invention, preferably from the selected host cell. Many specific and a variety of consensus RBSs are known, e.g., those described in and referenced by D. Frishman et al., Gene 234(2):257-65 (8 Jul. 1999); and B. E. Suzek et al., Bioinformatics 17(12):1123-30 (December 2001). In addition, either native or synthetic RBSs may be used, e.g., those described in: EP 0207459 (synthetic RBSs); O. Ikehata et al., Eur. J. Biochem. 181(3):563-70 (1989) (native RBS sequence of AAGGAAG). Further examples of methods, vectors, and translation and transcription elements, and other elements useful in the present invention are described in, e.g.: U.S. Pat. No. 5,055,294 to Gilroy and U.S. Pat. No. 5,128,130 to Gilroy et al.; U.S. Pat. No. 5,281,532 to Rammler et al.; U.S. Pat. Nos. 4,695,455 and 4,861,595 to Barnes et al.; U.S. Pat. No. 4,755,465 to Gray et al.; and U.S. Pat. No. 5,169,760 to Wilcox.

Transcription of the DNA encoding the heterologous protein of interest is increased by inserting an enhancer sequence into the vector or plasmid. Typical enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp in size that act on the promoter to increase its transcription. Examples include various Pseudomonas enhancers.

Generally, the heterologous expression vectors will include origins of replication and selectable markers permitting transformation of the host cell and a promoter derived from a highly-expressed gene to direct transcription of a downstream structural sequence. Such promoters can be derived from operons encoding the enzymes such as 3-phosphoglycerate kinase (PGK), acid phosphatase, or heat shock proteins, among others. Where signal sequences are used, the heterologous coding sequence is assembled in appropriate phase with translation initiation and termination sequences, and the signal sequence capable of directing compartmental accumulation or secretion of the translated protein. Optionally the heterologous sequence can encode a fusion enzyme including an N-terminal identification polypeptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed heterologous product. The fusion polypeptide can also comprise one or more target proteins or inhibitors or enhances thereof, as discussed supra.

Vectors are known in the art for expressing heterologous proteins in host cells, and any of these may be used for expressing the genes according to the present invention. Such vectors include, e.g., plasmids, cosmids, and phage expression vectors. Examples of useful plasmid vectors include, but are not limited to, the expression plasmids pBBR1MCS, pDSK519, pKT240, pML122, pPS10, RK2, RK6, pRO1600, and RSF1010. Other examples of such useful vectors include those described by, e.g.: N. Hayase, in Appl. Envir. Microbiol. 60(9):3336-42 (September 1994); A. A. Lushnikov et al., in Basic Life Sci. 30:657-62 (1985); S. Graupner & W. Wackemagel, in Biomolec. Eng. 17(1):11-16. (October 2000); H. P. Schweizer, in Curr. Opin. Biotech. 12(5):439-45 (October 2001); M. Bagdasarian & K. N. Timmis, in Curr. Topics Microbiol. Immunol. 96:47-67 (1982); T. Ishii et al., in FEMS Microbiol. Lett. 116(3):307-13 (Mar. 1, 1994); I. N. Olekhnovich & Y. K. Fomichev, in Gene 140(1):63-65 (Mar. 11, 1994); M. Tsuda & T. Nakazawa, in Gene 136(1-2):257-62 (Dec. 22, 1993); C. Nieto et al., in Gene 87(1):145-49 (Mar. 1, 1990); J. D. Jones & N. Gutterson, in Gene 61(3):299-306 (1987); M. Bagdasarian et al., in Gene 16(1-3):237-47 (December 1981); H. P. Schweizer et al., in Genet. Eng. (NY) 23:69-81 (2001); P. Mukhopadhyay et al., in J. Bact. 172(1):477-80 (January 1990); D. O. Wood et al., in J. Bact. 145(3):1448-51 (March 1981); and R. Holtwick et al., in Microbiology 147(Pt 2):337-44 (February 2001).

Further examples of expression vectors that can be useful in a host cell of the invention include those listed in Table 5 as derived from the indicated replicons.

TABLE 5 Examples of Useful Expression Vectors Replicon Vector(s) PPS10 PCN39, PCN51 RSF1010 PKT261-3 PMMB66EH PEB8 PPLGN1 PMYC1050 RK2/RP1 PRK415 PJB653 PRO1600 PUCP PBSP

The expression plasmid, RSF1010, is described, e.g., by F. Heffron et al., in Proc. Nat'l Acad. Sci. USA 72(9):3623-27 (September 1975), and by K. Nagahari & K. Sakaguchi, in J. Bact. 133(3):1527-29 (March 1978). Plasmid RSF1010 and derivatives thereof are particularly useful vectors in the present invention. Exemplary useful derivatives of RSF1010, which are known in the art, include, e.g., pKT212, pKT214, pKT231 and related plasmids, and pMYC1050 and related plasmids (see, e.g., U.S. Pat. Nos. 5,527,883 and 5,840,554 to Thompson et al.), such as, e.g., pMYC1803. Plasmid pMYC1803 is derived from the RSF1010-based plasmid pTJS260 (see U.S. Pat. No. 5,169,760 to Wilcox), which carries a regulated tetracycline resistance marker and the replication and mobilization loci from the RSF1010 plasmid. Other exemplary useful vectors include those described in U.S. Pat. No. 4,680,264 to Puhler et al.

In one embodiment, an expression plasmid is used as the expression vector. In another embodiment, RSF1010 or a derivative thereof is used as the expression vector. In still another embodiment, pMYC1050 or a derivative thereof, or pMYC4803 or a derivative thereof, is used as the expression vector.

The plasmid can be maintained in the host cell by inclusion of a selection marker gene in the plasmid. This may be an antibiotic resistance gene(s), where the corresponding antibiotic(s) is added to the fermentation medium, or any other type of selection marker gene known in the art, e.g., a prototrophy-restoring gene where the plasmid is used in a host cell that is auxotrophic for the corresponding trait, e.g., a biocatalytic trait such as an amino acid biosynthesis or a nucleotide biosynthesis trait, or a carbon source utilization trait.

The promoters used in accordance with the present invention may be constitutive promoters or regulated promoters. Common examples of useful regulated promoters include those of the family derived from the lac promoter (i.e. the lacZ promoter), especially the tac and trc promoters described in U.S. Pat. No. 4,551,433 to DeBoer, as well as Ptac16, Ptac17, PtacII, PlacUV5, and the T7lac promoter. In one embodiment, the promoter is not derived from the host cell organism. In certain embodiments, the promoter is derived from an E. coli organism.

Common examples of non-lac-type promoters useful in expression systems according to the present invention include, e.g., those listed in Table 6.

TABLE 6 Examples of non-lac Promoters Promoter Inducer P_(R) High temperature P_(L) High temperature Pm Alkyl- or halo-benzoates Pu Alkyl- or halo-toluenes Psal Salicylates

See, e.g.: J. Sanchez-Romero & V. De Lorenzo (1999) Manual of Industrial Microbiology and Biotechnology (A. Demain & J. Davies, eds.) pp. 460-74 (ASM Press, Washington, D.C.); H. Schweizer (2001) Current Opinion in Biotechnology, 12:439-445; and R. Slater & R. Williams (2000 Molecular Biology and Biotechnology (J. Walker & R. Rapley, eds.) pp. 125-54 (The Royal Society of Chemistry, Cambridge, UK)). A promoter having the nucleotide sequence of a promoter native to the selected bacterial host cell may also be used to control expression of the transgene encoding the target polypeptide, e.g, a Pseudomonas anthranilate or benzoate operon promoter (Pant, Pben). Tandem promoters may also be used in which more than one promoter is covalently attached to another, whether the same or different in sequence, e.g., a Pant-Pben tandem promoter (interpromoter hybrid) or a Plac-Plac tandem promoter, or whether derived from the same or different organisms.

Regulated promoters utilize promoter regulatory proteins in order to control transcription of the gene of which the promoter is a part. Where a regulated promoter is used herein, a corresponding promoter regulatory protein will also be part of an expression system according to the present invention. Examples of promoter regulatory proteins include: activator proteins, e.g., E. coli catabolite activator protein, MalT protein; AraC family transcriptional activators; repressor proteins, e.g., E. coli Lad proteins; and dual-function regulatory proteins, e.g., E. coli NagC protein. Many regulated-promoter/promoter-regulatory-protein pairs are known in the art. In one embodiment, the expression construct for the target protein(s) and the heterologous protein of interest are under the control of the same regulatory element.

Promoter regulatory proteins interact with an effector compound, i.e. a compound that reversibly or irreversibly associates with the regulatory protein so as to enable the protein to either release or bind to at least one DNA transcription regulatory region of the gene that is under the control of the promoter, thereby permitting or blocking the action of a transcriptase enzyme in initiating transcription of the gene. Effector compounds are classified as either inducers or co-repressors, and these compounds include native effector compounds and gratuitous inducer compounds. Many regulated-promoter/promoter-regulatory-protein/effector-compound trios are known in the art. Although an effector compound can be used throughout the cell culture or fermentation, in a preferred embodiment in which a regulated promoter is used, after growth of a desired quantity or density of host cell biomass, an appropriate effector compound is added to the culture to directly or indirectly result in expression of the desired gene(s) encoding the protein or polypeptide of interest.

By way of example, where a lac family promoter is utilized, a lacI gene can also be present in the system. The lacI gene, which is (normally) a constitutively expressed gene, encodes the Lac repressor protein (LacD protein) which binds to the lac operator of these promoters. Thus, where a lac family promoter is utilized, the lacI gene can also be included and expressed in the expression system. In the case of the lac promoter family members, e.g., the tac promoter, the effector compound is an inducer, preferably a gratuitous inducer such as IPTG (isopropyl-D-1-thiogalactopyranoside, also called “isopropylthiogalactoside”).

For expression of a protein or polypeptide of interest, any plant promoter may also be used. A promoter may be a plant RNA polymerase II promoter. Elements included in plant promoters can be a TATA box or Goldberg-Hogness box, typically positioned approximately 25 to 35 basepairs upstream (5′) of the transcription initiation site, and the CCAAT box, located between 70 and 100 basepairs upstream. In plants, the CCAAT box may have a different consensus sequence than the functionally analogous sequence of mammalian promoters (Messing et al. (1983) In: Genetic Engineering of Plants, Kosuge et al., eds., pp. 211-227). In addition, virtually all promoters include additional upstream activating sequences or enhancers (Benoist and Chambon (1981) Nature 290:304-310; Gruss et al. (1981) Proc. Nat. Acad. Sci. 78:943-947; and Khoury and Gruss (1983) Cell 27:313-314) extending from around −100 bp to −1,000 bp or more upstream of the transcription initiation site.

Expression Systems

It may be desirable to target the protein or polypeptide of interest to the periplasm of one or more of the populations of host cells in the array, or into the extracellular space. In one embodiment, the expression vector further comprises a nucleotide sequence encoding a secretion signal sequence polypeptide operably linked to the nucleotide sequence encoding the protein or polypeptide of interest. In some embodiments, no modifications are made between the signal sequence and the protein or polypeptide of interest. However, in certain embodiments, additional cleavage signals are incorporated to promote proper processing of the amino terminal of the polypeptide.

The vector can have any of the characteristics described above. In one embodiment, the vector comprising the coding sequence for the protein or polypeptide of interest further comprises a signal sequence, e.g., a secretion signal sequence.

Therefore, in one embodiment, this isolated polypeptide is a fusion protein of the secretion signal and a protein or polypeptide of interest. However, the secretion signal can also be cleaved from the protein when the protein is targeted to the periplasm. In one embodiment, the linkage between the Sec system secretion signal and the protein or polypeptide is modified to increase cleavage of the secretion signal.

Secretion signals useful in the compositions and methods of the present invention are known in the art and are provided herein and in U.S. Pat. App. Pub. Nos. 2006/0008877 and 2008/0193974, both incorporated herein by reference in there entirety. These sequences can promote the targeting of an operably linked polypeptide of interest to the periplasm of Gram-negative bacteria or into the extracellular environment. Use of secretion signal leader sequences can increase production of recombinant proteins in bacteria that produce improperly folded, aggregated or inactive proteins. Additionally, many types of proteins require secondary modifications that are inefficiently achieved using known methods. Secretion leader utilization can increase the harvest of properly folded proteins by secreting the protein from the intracellular environment. In Gram-negative bacteria, a protein secreted from the cytoplasm can end up in the periplasmic space, attached to the outer membrane, or in the extracellular broth. These methods also avoid formation of inclusion bodies, which constitute aggregated proteins. Secretion of proteins into the periplasmic space also has the well-known effect of facilitating proper disulfide bond formation (Bardwell et al. (1994) Phosphate Microorg. 270-5; Manoil (2000) Methods in Enzymol. 326: 35-47). Other benefits of secretion of recombinant protein include: more efficient isolation of the protein; proper folding and disulfide bond formation of the transgenic protein, leading to an increase in yield represented by, e.g., the percentage of the protein in active form, reduced formation of inclusion bodies and reduced toxicity to the host cell, and an increased percentage of the recombinant protein in soluble form. The potential for excretion of the protein of interest into the culture medium can also potentially promote continuous, rather than batch culture for protein production.

Certain secretion leader sequences useful in the compositions and methods of the present invention are shown in Table 7 below. As understood by those of skill in the art, these sequences and others described in the art can retain function or have improved function when amino acid changes are made. Furthermore, it is understood that the nucleic acid sequences encoding these leaders can in come cases vary without effect on the function of the leader. Additional leader sequences are provided in the sequence listings.

TABLE 7 Exemplary Leader Sequences SEQ ID Leader Sequence Abbrev Amino Acid Sequence NO Porin E1 PorE MKKSTLAVAVTLGAIAQQAGA Outer membrane OprF MKLKNTLGLAIGSLIAATSFGVLA porin F Periplasmic Pbp MKLKRLMAAMTFVAAGVATANAVA phosphate binding protein Azurin Azu MFAKLVAVSLLTLASGQLLA Lipoprotein B Lip MIKRNLLVMGLAVLLSA RXF04720 Lysine-arginine- Lao MQNYKKFLLAAAVSMAFSATAMA ornithine-binding protein Iron(III) binding Ibp MIRDNRLKTSLLRGLTLTLLSLTLLSPAAHS protein PB signal sequence Pbp- MKLKRLMAAMTFVAAGVATVNAVA mutant A20V DsbA DsbA MRNLILSAALVTASLFGMTAQA DsbC DsbC MRLTQIIAAAAIALVSTFALA tolB tolB MRNLLRGMLVVICCMAGIAAA (PCR amplified from MB214 genomic) Tetratricopeptide tpr MNRSSALLLAFVFLSGCQAMA repeat family protein Methyl-accepting MSLRNMNIAPRAFLGFAFIGALMLLLGVFALNQMSKIRA chemotaxis protein Toluene tolerance ttg2C MQNRTVEIGVGLFLLAGILALLLLALRVSGLSA protein ttg2C FlgI FlgI MKFKQLMAMALLLALSAVAQA RXF05262 EcpD, CupC2 cupC2 MPPRSIAACLGLLGLLMATQAAA bacterial pili assembly chaperone RXF04554 EcpD, CupB2 cupB2 MLFRTLLASLTFAVIAGLPSTAHA RXF05310 EcpD, CupA2 cupA2 MSCTRAFKPLLLIGLATLMCSHAFA RXF04296 NikA nikA MRLAALPLLLAPLFIAPMAVA Periplasmic dipeptide transport protein RXF08966 Bce bce MSTRIPRRQWLKGASGLLAAASLGRLANREARA (Bacillus coagulans) IBP S31A MIRDNRLKTSLLRGLTLTLLSLTLLSPAAHA

In embodiments, the expression vector contains an optimal ribosome binding sequence. Modulating translation strength by altering the translation initiation region of a protein of interest can be used to improve the production of heterologous cytoplasmic proteins that accumulate mainly as inclusion bodies due to a translation rate that is too rapid. Secretion of heterologous proteins into the periplasmic space of bacterial cells can also be enhanced by optimizing rather than maximizing protein translation levels such that the translation rate is in sync with the protein secretion rate.

The translation initiation region has been defined as the sequence extending immediately upstream of the ribosomal binding site (RBS) to approximately 20 nucleotides downstream of the initiation codon (McCarthy et al. (1990) Trends in Genetics 6:78-85, herein incorporated by reference in its entirety). In prokaryotes, alternative RBS sequences can be utilized to optimize translation levels of heterologous proteins by providing translation rates that are decreased with respect to the translation levels using the canonical, or consensus, RBS sequence (AGGAGG; SEQ ID NO:1) described by Shine and Dalgarno (Proc. Natl. Acad. Sci. USA 71:1342-1346, 1974). By “translation rate” or “translation efficiency” is intended the rate of mRNA translation into proteins within cells. In most prokaryotes, the Shine-Dalgarno sequence assists with the binding and positioning of the 30S ribosome component relative to the start codon on the mRNA through interaction with a pyrimidine-rich region of the 16S ribosomal RNA. The RBS (also referred to herein as the Shine-Dalgarno sequence) is located on the mRNA downstream from the start of transcription and upstream from the start of translation, typically from 4 to 14 nucleotides upstream of the start codon, and more typically from 8 to 10 nucleotides upstream of the start codon. Because of the role of the RBS sequence in translation, there is a direct relationship between the efficiency of translation and the efficiency (or strength) of the RBS sequence.

In some embodiments, modification of the RBS sequence results in a decrease in the translation rate of the heterologous protein. This decrease in translation rate may correspond to an increase in the level of properly processed protein or polypeptide per gram of protein produced, or per gram of host protein. The decreased translation rate can also correlate with an increased level of recoverable protein or polypeptide produced per gram of recombinant or per gram of host cell protein. The decreased translation rate can also correspond to any combination of an increased expression, increased activity, increased solubility, or increased translocation (e.g., to a periplasmic compartment or secreted into the extracellular space). In this embodiment, the term “increased” is relative to the level of protein or polypeptide that is produced, properly processed, soluble, and/or recoverable when the protein or polypeptide of interest is expressed under the same conditions, and wherein the nucleotide sequence encoding the polypeptide comprises the canonical RBS sequence. Similarly, the term “decreased” is relative to the translation rate of the protein or polypeptide of interest wherein the gene encoding the protein or polypeptide comprises the canonical RBS sequence. The translation rate can be decreased by at least about 5%, at least about 10%, at least about 15%, at least about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70, at least about 75% or more, or at least about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 6-fold, about 7-fold, or greater.

In some embodiments, the RBS sequence variants described herein can be classified as resulting in high, medium, or low translation efficiency. In one embodiment, the sequences are ranked according to the level of translational activity compared to translational activity of the canonical RBS sequence. A high RBS sequence has about 60% to about 100% of the activity of the canonical sequence. A medium RBS sequence has about 40% to about 60% of the activity of the canonical sequence. A low RBS sequence has less than about 40% of the activity of the canonical sequence.

Examples of RBS sequences are shown in Table 8. The sequences were screened for translational strength using COP-GFP as a reporter gene and ranked according to percentage of consensus RBS fluorescence. Each RBS variant was placed into one of three general fluorescence ranks: High (“Hi”—100% Consensus RBS fluorescence), Medium (“Med”—46-51% of Consensus RBS fluorescence), and Low (“Lo”—16-29% Consensus RBS fluorescence).

TABLE 8 RBS Sequences Consensus AGGAGG High RBS2 GGAGCG Med RBS34 GGAGCG Med RBS41 AGGAGT Med RBS43 GGAGTG Med RBS48 GAGTAA Low RBS1 AGAGAG Low RBS35 AAGGCA Low RBS49 CCGAAC Low

Methods for identifying optimal ribosome binding sites are described in U.S. Pat. App. No. 2009/062143, “Translation initiation region sequences for optimal expression of heterologous proteins,” incorporated herein by reference in its entirety.

One or more genes encoding heterologous proteins can be expressed from the same expression vector, as desired. For example, one might choose to express an antibody heavy chain and light chain from the same vector. The same promoter and regulatory sequences can be used to drive expression of both genes (e.g., in tandem), or the genes can be expressed separately on the same expression vector. In embodiments of the invention, at least two genes are encoded on separate expression vectors within the same expression system. The at least two genes are related or unrelated.

In the context of the array, it can be convenient and informative to test the expression of a group of heterologous proteins in parallel in the same array. This can be accomplished by providing several series of expression systems. One series contains expression vectors encoding at least one heterologous protein to be compared with at least one other heterologous protein in another series of expression systems. For example, a group of variants of the same protein can be tested on the same array in several series of expression systems. In each series of expression systems, the expression vector encodes the same variant. Such an approach could also be useful for testing a library of binding proteins, e.g., antibodies. In embodiments, the proteins tested in parallel are related; in others, they are not.

Prior to cloning into an expression vector, the protein coding sequence can be optimized if desired. The sequence is cloned into a series of expression vectors containing, e.g., secretion leader sequences and other appropriate promoters or regulatory sequences as described herein. These sequence elements can be selected based on an analysis of the heterologous protein amino acid sequence as described herein.

The CHAMPION™ pET expression system provides a high level of protein production. Expression is induced from the strong T7lac promoter. This system takes advantage of the high activity and specificity of the bacteriophage T7 RNA polymerase for high level transcription of the gene of interest. The lac operator located in the promoter region provides tighter regulation than traditional T7-based vectors, improving plasmid stability and cell viability (Studier and Moffatt (1986) J Molecular Biology 189(1): 113-30; Rosenberg, et al. (1987) Gene 56(1): 125-35). The T7 expression system uses the T7 promoter and T7 RNA polymerase (T7 RNAP) for high-level transcription of the gene of interest. High-level expression is achieved in T7 expression systems because the T7 RNAP is more processive than native E. coli RNAP and is dedicated to the transcription of the gene of interest. Expression of the identified gene is induced by providing a source of T7 RNAP in the host cell. This is accomplished by using a BL21 E. coli host containing a chromosomal copy of the T7 RNAP gene. The T7 RNAP gene is under the control of the lacUV5 promoter which can be induced by IPTG. T7 RNAP is expressed upon induction and transcribes the gene of interest.

The pBAD expression system allows tightly controlled, titratable expression of protein or polypeptide of interest through the presence of specific carbon sources such as glucose, glycerol and arabinose (Guzman, et al. (1995) J Bacteriology 177(14): 4121-30). The pBAD vectors are uniquely designed to give precise control over expression levels. Heterologous gene expression from the pBAD vectors is initiated at the araBAD promoter. The promoter is both positively and negatively regulated by the product of the araC gene. AraC is a transcriptional regulator that forms a complex with L-arabinose. In the absence of L-arabinose, the AraC dimer blocks transcription. For maximum transcriptional activation two events are required: (i) L-arabinose binds to AraC allowing transcription to begin, and, (ii) The cAMP activator protein (CAP)-cAMP complex binds to the DNA and stimulates binding of AraC to the correct location of the promoter region.

The trc expression system allows high-level, regulated expression in E. coli from the trc promoter. The trc expression vectors have been optimized for expression of eukaryotic genes in E. coli. The trc promoter is a strong hybrid promoter derived from the tryptophane (trp) and lactose (lac) promoters. It is regulated by the lacO operator and the product of the lacIQ gene (Brosius, J. (1984) Gene 27(2): 161-72).

Transformation of the host cells with the vector(s) disclosed herein may be performed using any transformation methodology known in the art, and the bacterial host cells may be transformed as intact cells or as protoplasts (i.e. including cytoplasts). Exemplary transformation methodologies include poration methodologies, e.g., electroporation, protoplast fusion, bacterial conjugation, and divalent cation treatment, e.g., calcium chloride treatment or CaCl/Mg2+ treatment, or other well known methods in the art. See, e.g., Morrison, J. Bact., 132:349-351 (1977); Clark-Curtiss & Curtiss, Methods in Enzymology, 101:347-362 (Wu et al., eds, 1983), Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd ed. 1989); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., eds., 1994)).

Proteins of Interest

The methods and compositions of the present invention are useful for identifying a P. fluorescens strain that is optimal for producing high levels of a properly processed protein or polypeptide of interest. The arrays are useful for screening for production of a protein or polypeptide of interest of any species and of any size. However, in certain embodiments, the protein or polypeptide of interest is a therapeutically useful protein or polypeptide. In some embodiments, the protein can be a mammalian protein, for example a human protein, and can be, for example, a growth factor, a cytokine, a chemokine or a blood protein. The protein or polypeptide of interest can be processed in a similar manner to the native protein or polypeptide. In certain embodiments, the protein or polypeptide of interest is less than 100 kD, less than 50 kD, or less than 30 kD in size. In certain embodiments, the protein or polypeptide of interest is a polypeptide of at least about 5, 10, 15, 20, 30, 40, 50 or 100 or more amino acids.

The coding sequence for the protein or polypeptide of interest can be a native coding sequence for the polypeptide, if available, but will more preferably be a coding sequence that has been selected, improved, or optimized for use in an expressible form in the strains of the array: for example, by optimizing the gene to reflect the codon use bias of a Pseudomonas species such as P. fluorescens or other suitable organism. For gene optimization, one or more rare codons may be removed to avoid ribosomal stalling and minimize amino acid misincorporation. One or more gene-internal ribosome binding sites may also be eliminated to avoid truncated protein products. Long stretches of C and G nucleotides may be removed to avoid RNA polymerase slippage that could result in frame-shifts. Strong gene-internal stem-loop structures, especially the ones covering the ribosome binding site, may also be eliminated.

In other embodiments, the protein when produced also includes an additional targeting sequence, for example a sequence that targets the protein to the periplasm or the extracellular medium. In one embodiment, the additional targeting sequence is operably linked to the carboxy-terminus of the protein. In another embodiment, the protein includes a secretion signal for an autotransporter, a two partner secretion system, a main terminal branch system or a fimbrial usher porin.

The gene(s) that result are constructed within or are inserted into one or more vectors, and then transformed into each of the host cell populations in the array. Nucleic acid or a polynucleotide said to be provided in an “expressible form” means nucleic acid or a polynucleotide that contains at least one gene that can be expressed by the one or more of the host cell populations of the invention.

Extensive sequence information required for molecular genetics and genetic engineering techniques is widely publicly available. Access to complete nucleotide sequences of mammalian, as well as human, genes, cDNA sequences, amino acid sequences and genomes can be obtained from GenBank. GenBank is maintained by the National Institutes of Health, Bethesda, Md., and can be accessed at ncbi.nlm.nih.gov/Entrez within the NIH website. Additional information can also be obtained from GeneCards, an electronic encyclopedia integrating information about genes and their products and biomedical applications, made available by the Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, Israel. Nucleotide sequence information also can be obtained from the EMBL Nucleotide Sequence Database made available on the worldwide web by the European Bioinformatics Institute (Hinxton, Cambridge, UK) or from the DNA Databank of Japan (Research Organization of Information and Systems, National Institute of Genetics, Center for Information Biology and DNA Data Bank of Japan, 1111 Yata, Mishima, Shizuoka 411-8540, Japan). Additional sites for information on amino acid sequences include the Protein Information Resource website established by the National Biomedical Research Foundation, which includes Swiss-Prot.

Examples of proteins that can be expressed in this invention include molecules such as, e.g., renin, a growth hormone, including human growth hormone; bovine growth hormone; growth hormone releasing factor; parathyroid hormone; thyroid stimulating hormone; lipoproteins; α-1-antitrypsin; insulin A-chain; insulin B-chain; proinsulin; thrombopoietin; follicle stimulating hormone; calcitonin; luteinizing hormone; glucagon; clotting factors such as factor VIIIC, factor IX, tissue factor, and von Willebrands factor; anti-clotting factors such as Protein C; atrial naturietic factor; lung surfactant; a plasminogen activator, such as urokinase or human urine or tissue-type plasminogen activator (t-PA); bombesin; thrombin; hemopoietic growth factor; tumor necrosis factor-alpha and -beta; enkephalinase; a serum albumin such as human serum albumin; mullerian-inhibiting substance; relaxin A-chain; relaxin B-chain; prorelaxin; mouse gonadotropin-associated polypeptide; a microbial protein, such as beta-lactamase; Dnase; inhibin; activin; vascular endothelial growth factor (VEGF); receptors for hormones or growth factors; integrin; protein A or D; rheumatoid factors; a neurotrophic factor such as brain-derived neurotrophic factor (BDNF), neurotrophin-3, -4, -5, or -6 (NT-3, NT-4, NT-5, or NT-6), or a nerve growth factor such as NGF-β; cardiotrophins (cardiac hypertrophy factor) such as cardiotrophin-1 (CT-1); platelet-derived growth factor (PDGF); fibroblast growth factor such as aFGF and bFGF; epidermal growth factor (EGF); transforming growth factor (TGF) such as TGF-alpha and TGF-β, including TGF-β1, TGF-β2, TGF-β3, TGF-β4, or TGF-β5; insulin-like growth factor-I and -II (IGF-I and IGF-II); des(1-3)-IGF-I (brain IGF-I), insulin-like growth factor binding proteins; CD proteins such as CD-3, CD-4, CD-8, and CD-19; erythropoietin; osteoinductive factors; immunotoxins; a bone morphogenetic protein (BMP); an interferon such as interferon-alpha, -beta, and -gamma; colony stimulating factors (CSFs), e.g., M-CSF, GM-CSF, and G-CSF; interleukins (ILs), e.g., IL-1 to IL-10; anti-HER-2 antibody; superoxide dismutase; T-cell receptors; surface membrane proteins; decay accelerating factor; viral antigen such as, for example, a portion of the AIDS envelope; transport proteins; homing receptors; addressins; regulatory proteins; antibodies; and fragments of any of the above-listed polypeptides.

In certain embodiments, the protein or polypeptide can be selected from IL-1, IL-1a, IL-1b, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-12elasti, IL-13, IL-15, IL-16, IL-18, IL-18BPa, IL-23, IL-24, VIP, erythropoietin, GM-CSF, G-CSF, M-CSF, platelet derived growth factor (PDGF), MSF, FLT-3 ligand, EGF, fibroblast growth factor (FGF; e.g., α-FGF (FGF-1), β-FGF (FGF-2), FGF-3, FGF-4, FGF-5, FGF-6, or FGF-7), insulin-like growth factors (e.g., IGF-1, IGF-2); tumor necrosis factors (e.g., TNF, Lymphotoxin), nerve growth factors (e.g., NGF), vascular endothelial growth factor (VEGF); interferons (e.g., IFN-α, IFN-β, IFN-γ); leukemia inhibitory factor (LIF); ciliary neurotrophic factor (CNTF); oncostatin M; stem cell factor (SCF); transforming growth factors (e.g., TGF-α, TGF-β1, TGF-β2, TGF-β3); TNF superfamily (e.g., LIGHT/TNFSF14, STALL-1/TNFSF13B (BLy5, BAFF, THANK), TNFalpha/TNFSF2 and TWEAK/TNFSF12); or chemokines (BCA-1/BLC-1, BRAK/Kec, CXCL16, CXCR3, ENA-78/LIX, Eotaxin-1, Eotaxin-2/MPIF-2, Exodus-2/SLC, Fractalkine/Neurotactin, GROalpha/MGSA, HCC-1, I-TAC, Lymphotactin/ATAC/SCM, MCP-1/MCAF, MCP-3, MCP-4, MDC/STCP-1/ABCD-1, MIP-1.quadrature., MIP-1.quadrature., MIP-2.quadrature./GRO.quadrature., MIP-3.quadrature./Exodus/LARC, MIP-3/Exodus-3/ELC, MIP-4/PARC/DC-CK1, PF-4, RANTES, SDF1, TARC, TECK, microbial toxins, ADP ribosylating toxins, microbial or viral antigens).

In one embodiment of the present invention, the protein of interest can be a multi-subunit protein or polypeptide. Multisubunit proteins that can be expressed include homomeric and heteromeric proteins. The multisubunit proteins may include two or more subunits that may be the same or different. For example, the protein may be a homomeric protein comprising 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more subunits. The protein also may be a heteromeric protein including 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more subunits. Exemplary multisubunit proteins include: receptors including ion channel receptors; extracellular matrix proteins including chondroitin; collagen; immunomodulators including MHC proteins, full chain antibodies, and antibody fragments; enzymes including RNA polymerases, and DNA polymerases; and membrane proteins.

In another embodiment, the protein of interest can be a blood protein. The blood proteins expressed in this embodiment include but are not limited to carrier proteins, such as albumin, including human and bovine albumin, transferrin, recombinant transferrin half-molecules, haptoglobin, fibrinogen and other coagulation factors, complement components, immunoglobulins, enzyme inhibitors, precursors of substances such as angiotensin and bradykinin, insulin, endothelin, and globulin, including alpha, beta, and gamma-globulin, and other types of proteins, polypeptides, and fragments thereof found primarily in the blood of mammals. The amino acid sequences for numerous blood proteins have been reported (see, S. S. Baldwin (1993) Comp. Biochem Physiol. 106b:203-218), including the amino acid sequence for human serum albumin (Lawn, L. M., et al. (1981) Nucleic Acids Research, 9:6103-6114.) and human serum transferrin (Yang, F. et al. (1984) Proc. Natl. Acad. Sci. USA 81:2752-2756).

In another embodiment, the protein of interest can be an enzyme or co-factor. The enzymes and co-factors expressed in this embodiment include but are not limited to aldolases, amine oxidases, amino acid oxidases, aspartases, B12 dependent enzymes, carboxypeptidases, carboxyesterases, carboxylyases, chemotrypsin, CoA requiring enzymes, cyanohydrin synthetases, cystathione synthases, decarboxylases, dehydrogenases, alcohol dehydrogenases, dehydratases, diaphorases, dioxygenases, enoate reductases, epoxide hydrases, fumerases, galactose oxidases, glucose isomerases, glucose oxidases, glycosyltrasferases, methyltransferases, nitrile hydrases, nucleoside phosphorylases, oxidoreductases, oxynitilases, peptidases, glycosyltrasferases, peroxidases, enzymes fused to a therapeutically active polypeptide, tissue plasminogen activator; urokinase, reptilase, streptokinase; catalase, superoxide dismutase; Dnase, amino acid hydrolases (e.g., asparaginase, amidohydrolases); carboxypeptidases; proteases, trypsin, pepsin, chymotrypsin, papain, bromelain, collagenase; neuramimidase; lactase, maltase, sucrase, and arabinofuranosidases.

In another embodiment, the protein of interest can be a single chain, Fab fragment and/or full chain antibody or fragments or portions thereof. A single-chain antibody can include the antigen-binding regions of antibodies on a single stably-folded polypeptide chain. Fab fragments can be a piece of a particular antibody. The Fab fragment can contain the antigen binding site. The Fab fragment can contain 2 chains: a light chain and a heavy chain fragment. These fragments can be linked via a linker or a disulfide bond.

In other embodiments, the protein of interest is a protein that is active at a temperature from about 20 to about 42° C. In one embodiment, the protein is active at physiological temperatures and is inactivated when heated to high or extreme temperatures, such as temperatures over 65° C.

In one embodiment, the protein of interest is a protein that is active at a temperature from about 20 to about 42° C., and/or is inactivated when heated to high or extreme temperatures, such as temperatures over 65° C.; is, or is substantially homologous to, a native protein, such as a native mammalian or human protein and not expressed from nucleic acids in concatameric form, where the promoter is not a native promoter in to the host cell used in the array but is derived from another organism, such as E. coli.

The heterologous protein(s) expressed using the compositions and methods of the invention can be any protein wished to be overexpressed, e.g., a protein that has been found to to be difficult to express. Such a protein may have been found to form inclusion bodies, aggregate, be degraded, or otherwise be produced in an unsatisfactory manner in previous attempts at overexpression. The protein may have been predicted to be insoluble based on analysis of the amino acid sequence. It is known to those of skill in the art that the propensity for a protein to be insoluble can be evaluated using prediction tools available to those of skill in the art. Prediction tools include, e.g., PROSO, described by Smialowski, et al., 2007, “Protein solubility: sequence based prediction and experimental verification,” Bioinformatics 23(19):2536. PROSO can be used to assess the chance that a protein will be soluble upon heterologous expression in E. coli. The sequence-based approach classifies proteins as “soluble” or “insoluble.” Another tool is SOLpro, described by Magnan, et al., 2009, “SOLpro: accurate sequence-based prediction of protein solubility,” Bioinformatics 25(17):2200-2207. SOLpro predicts the propensity of a protein to be soluble upon overexpression in E. coli. It is integrated in the SCRATCH suite of predictors and is available for download as a standalone application and for use at the Scratch proteomics website.

Table 9 lists exemplary heterologous proteins that can be expressed using the methods and arrays of the present invention, and includes examples of references and sequence information relating to proteins listed. The lists of exemplary proteins and exemplary sequences provided, in Table 8 and elsewhere herein, are in no way intended to be limiting. It is understood that the compositions and methods of the invention can be used in the expression of any desired protein.

TABLE 9 Exemplary Heterologous Proteins Exemplary References/Sequences Protein Class Exemplary Protein (incorporated herein by reference) Vertebrate and ω-Agatoxin Swiss-Prot Acc. No. P15969 (omega Invertebrate Animal μ-Agatoxin agatoxin 1A) Toxins Swiss-Prot: P15970 (omega agatoxin 1B) Agitoxin Allopumiliotoxin 267A ω-Atracotoxin-HV1 δ-Atracotoxin-Hv1b Batrachotoxin (Dendrobatidae frogs) Botrocetin (Bothrops jararaca) Usami, et al., 1993, “Primary structure of two-chain botrocetin, a von Willebrand factor modulator purified from the venom of Bothrops jararaca,” Proc. Natl. Acad. Sci. USA 90: 928-932 Bufotoxins (Arenobufagin, Bufotalin, Bufotenin · Cinobufagin, Marinobufagin) Bungarotoxin (Alpha-Bungarotoxin, Beta-Bungarotoxin) Calcicludine Calciseptine Cardiotoxin III Catrocollastatin C (Crotalus atrox) Calvete, et al., 2000, “The disulfide bond pattern of catrocollastatin C, a disintegrin- like/cysteine-rich protein isolated from Crotalus atrox venom,” Protein Science 9: 1365-1373 Charybdotoxin Ciguatera Cobra venom cytotoxins Chiou, et al., 1993, “Cobra venom cardiotoxin (cytotoxin) isoforms and neurotoxin: Comparative potency of protein kinase C inhibition and cancer cell cytotoxicity and modes of enzyme inhibition,” Biochemistry, 32 (8), pp 2062-2067 Conotoxin Echinoidin (Anthocidaris crassispina) Eledoisin Epibatidine Fibrolase (Agkistrodon contortrix Randolph, et al., 1992, “Amino acid contortrix) sequence of fibrolase, a direct-acting fibrinolytic enzyme from Agkistrodon contortrix contortrix venom,” Protein Science 1 590-600 Hefutoxin Histrionicotoxin Huwentoxin-I Huwentoxin-II (Selenocosmia Shu, et al., 2002, “The structure of spider huwena) toxin huwentoxin-II with unique disulfide linkage: Evidence for structural evolution,” Protein Science 11: 245-252 J-ACTX-Hv1c Kunitz-Type Toxins, e.g. Yuan, et al., 2008, “Discovery of a distinct Dendrotoxin-K, Dendrotoxin 1 superfamily of Kunitz-type toxin (KTT) from tarantulas,” PLoS one 3(10): e3414, doi: 10.1371/journal.pone.0003414 Latrotoxin (Alpha-latrotoxin) Margatoxin Maurotoxin Onchidal PhTx3 Pumiliotoxin 251D Rattlesnake lectin Robustoxin Saxitoxin Scyllatoxin Slotoxin Stromatoxin Taicatoxin Tarichatoxin Tetrodotoxin (e.g., toads, Tetraodontiformes fish, Naticidae sea snails, newts, Vibrio bacteria) Plant toxins Ricin (Ricinus communis) GenBank Nucleotide Acc. No. DQ661048 (Ricin A chain) Halling, et al., 1985, “Genomic cloning and characterization of a ricin gene from Ricinus communis” Nucleic Acids Res. 13(22): 8019-33 (Sequence on p. 8025) Gelonin (Gelonium multiflorum) GenBank Acc. No. L12243 Fungal toxins Aflatoxin Amatoxin (Alpha-amanitin, Beta- amanitin, Gamma-amanitin, Epsilon-amanitin) Citrinin Cytochalasin Ergotamine Fumagillin Fumonisin (Fumonisin B1, Fumonisin B2) Gliotoxin GenBank Acc. No. AAW03299 (gliotoxin) Gardiner, et al., 2005, “Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster of Aspergillus fumigatus, FEMS Microbiol. Lett. 248(2): 241-248 Tsunawaki, et al., 2004, “Fungal metabolite gliotoxin inhibits assembly of the human respiratory burst NADPH oxidase,” Infection and Immunity 72(6): 3373-3382 Helvolic Acid Ibotenic acid Muscimol Ochratoxin Patulin Sterigmatocystin Trichothecene Vomitoxin Zeranol Zearalenone Bacterial toxins Bacillus anthracis toxins: e.g., Swiss-Prot Acc. No. P13423.2 (rPA, Anthrax toxin, Adenylate cyclase, Protective Antigen) rPA Bacillus thuringiensis: Cry toxins GenBank accession numbers for Cry proteins listed in, e.g., Table 1 of U.S. Pat. No. 6,642,030, “Nucleic acid compositions encoding modified Bacillus thuringiensis coleopteran-toxic crystal proteins” Bordetella pertussis: Pertussis toxin EMBL M13223 (pertussis toxin operon of 5 Pertussis toxin variants ORFs) U.S. Pat. No. 5,085,862, “Genetic detoxification of pertussis toxin” U.S. Pat. No. 5,165,927, “Composition with modified pertussis toxin” U.S. Pat. No. 5,773,600, “DNA encoding pertussis toxin muteins” Clostridium botulinum: Botulinum Fischer, et al., 2007, “Crucial role of the toxins disulfide bridge between botulinum neurotoxin light and heavy chains in protease translocation across membranes,” J. Biol. Chem. 282(40): 29604-11, Epub, Baldwin, et al., 2008, “Subunit vaccine against the seven serotypes of botulism,” Infection and Immunity 76(3): 1314-1318 Clostridium difficile: Toxin A, B Swiss-Prot Acc. No. P16154 (wild type Wild type, variants, mutants Toxin A, strain VPI) Swiss-Prot Acc. No. P18177 (wild type Toxin B, strain VPI) US Pat. App. Pub. Nos. 2004/0028705 and 2008/0107673, “Mutants of clostridium difficile toxin B and methods of use” Clostridium perfringens: Alpha toxin, Enterotoxin Clostridium tetani: Tetanus toxin GenBank Acc. No. 1A8D_A U.S. Pat. No. 5,571,694, “Expression of tetanus toxin fragment C in yeast” U.S. Pat. No. 6,372,225, “Tetanus toxin functional fragment antigen and tetanus vaccine” Schiavo, et al., 1990, “An intact interchain disulfide bond is required for the neurotoxicity of tetanus toxin,” Infection and Immunity 58(12): 4136-4141 U.S. Pat. No. 7,556,817, “Clostridial toxin activatable Clostridial toxins” Corynebacterium beta: Diphtheria GenBank Acc. No. K01722 (DT nucleotide) toxin (DT) GenBank Acc. No. AAA32182 (DT protein) Greenfield, et al., 1983, “Nucleotide sequence of the structural gene for diphtheria toxin carried by corynebacteriophage beta,” Proc. Natl. Acad. Sci. U.S.A. 80(22): 6853-6857 Papini, et al., 1993, “Cell penetration of diphtheria toxin. Reduction of the interchain disulfide bridge is the rate-limiting step of translocation in the cytosol,” J. Biol. Chem. 268(3): 1567-74 Diphtheria toxin variants, e.g., GenBank Acc. No. 1007216A (CRM197) CRM45, CRM176, CRM197 GenBank Acc. No. 1007216B (CRM45) U.S. Pat. No. 7,585,942, “Diphtheria toxin variant” Orr, et al., 1999, “Expression and Immunogenicity of a Mutant Diphtheria Toxin Molecule, CRM 197, and Its Fragments in Salmonella typhi Vaccine Strain CVD 908-htrA,” Infection and Immunity 67(8): 4290-4294 Giannini, et al., 1984, “The amino-acid sequence of two non-toxic mutants of diphtheria toxin: CRM45 and CRM197,” Nucleic Acids Research 12(10): 4063-4069 E. coli: GenBank Acc. No. AAA24685 (Heat-labile Verotoxin/Shiga-like toxin enterotoxin A prepeptide) Heat-stable enterotoxin GenBank Acc. No. AAC60441 (Heat-labile Heat-labile enterotoxin enterotoxin B subunit; LTc B subunit) Enterotoxins Listeria monocytogenes: Listeriolysin O Mycobacterium tuberculosis: Cord factor Pseudomonas exotoxin Salmonella endotoxin, exotoxin Shigella disinteriae: Shiga toxin Staphylococcus aureus: Alpha/beta/delta toxin Exfoliatin Toxin Toxic shock syndrome toxin Enterotoxins Leukocidin (Panton-Valentine leukocidin) Streptococcus pyogenes: Akao, et al., 1999, “Unique synthetic Streptolysin S peptides stimulating streptolysin S production in streptococci,” J. Biochem. 125(1): 27-30 Akao, et al., 1992, “Purification and characterization of a peptide essential for formation of streptolysin S by Streptococcus pyogenes,” Infection and Immunity 60(11): 4777-4780 Vibrio cholerae: Cholera toxin GenBank Acc. No. ACH70471 Tsai, et al., 2002, “Unfolded cholera toxin is transferred to the ER membrane and released from protein disulfide isomerase upon oxidation by Ero1,” J. Cell Biology 159(2): 207-215 Toxin-like proteins “ClanTox: a classifier of short animal toxins,” Nucleic Acids Research 37, Web Server issue W363-W368 doi: 10.1093/nar/gkp299. Cytokines Interferon alpha 2a Swiss-Prot P01563 (Receptors and (mature form amino acids 24-188) Ligands) Interferon alpha 2b GenBank Acc. No. NP_000596 (mature form amino acids 24-188) U.S. Pat. No. 7,189,389, “Pharmaceutical composition of human interferon-alpha 2 and interferon- alpha 8 subtypes” Interferon beta GenBank Acc. No. ABS89222 U.S. Pat. No. 7,399,463, “HSA-free formulations of interferon-beta” Interferon gamma GenBank Acc. No. NP_000610 (mature form aa 24-166) U.S. Pat. No. 7,524,931, “Full-length interferon gamma polypeptide variants” U.S. Pat. No. 7,504,237, “Polynucleotides encoding interferon gamma polypeptides” Interleukin 1 beta GenBank Acc. No. NP_000567 (mature form aa 117-269) Interleukin 6 GenBank Acc. No. AAC41704 U.S. Pat. No. 7,560,112, “Anti-il-6 antibodies, compositions, methods and uses” Tumor Necrosis Factor Family, e.g., GenBank Acc. No. CAA26669.1 (human TNFα TNF-alpha) TNFβ (formerly LTα) (mature form aa 77-233) LTβ PCT WO 2005/103077 TRELL Amino acid sequences for human TNF, LT- FasL α, LT-β, FasL, TFRP, TRAIL, CD27L, CD40L CD30L, CD40L, and 4-1BBL and TRELL CD30L provided by, e.g., U.S. Pat. No. 7,566,769,” CD27L Tumor necrosis factor related ligand” 4-1BBL GenBank Acc. No. AAA61198 (human TNF-related apoptosis-inducing tumor necrosis factor) ligand (TRAIL) Wang, et al., 1985, “Molecular cloning of RANKL (also TRANCE) the complementary DNA for human tumor GITRL necrosis factor,” Science 228 (4696), 149-154 TNF-2 GenBank Acc. No. AAA61200 (human TFRP tumor necrosis factor) OX40L Nedospasov, et al., 1986, “Tandem arrangement of genes coding for tumor necrosis factor (TNF-alpha) and lymphotoxin (TNF-beta) in the human genome,” Cold Spring Harb. Symp. Quant. Biol. 51 Pt 1, 611-624 U.S. Pat. No. 7,544,519, “Fhm a novel member of the TNF ligand supergene family: materials and methods for interaction modulators” Mouse and human RANKL sequences provided in, e.g., U.S. Pat. No. 7,411,050, “Monoclonal blocking antibody to human RANKL” GenBank Acc. No. AB008426 (mouse RANKL) Yasuda, et al., 1998, “Osteoclast differentiation factor is a ligand for osteoprotegerin/osteoclastogenesis- inhibitory factor and is identical to TRANCE/RANKL,” Proc. Natl. Acad. Sci. U.S.A. 95(7), 3597-3602 Anderson, et al., 1997, “A homologue of the TNF receptor and its ligand enhance T-cell growth and dendritic-cell function,” Nature 390 (6656), 175-179 Antibodies/Antibody Modified anti-TNF-alpha antibody U.S. Pat. No. 6,015,557, “Tumor necrosis factor Derivatives Infliximab (Remicade) antagonists for the treatment of neurological disorders” Nagahira, et al., Humanization of a mouse neutralizing monoclonal antibody against tumor necrosis factor-alpha (TNF-alpha), J Immunol Methods. 1999 Jan 1; 222(1-2): 83-92 Knight, et al., Construction and initial characterization of a mouse-human chimeric anti-TNF antibody. Mol Immunol. 1993 Nov; 30(16): 1443-53. Golimumab (Simponi) Adalimumab (Humira) Diabodies EP 0 404 097, “Bispecific and oligospecific, mono- and oligovalent receptors, production and applications thereof” WO 93/11161, “Multivalent antigen- binding proteins” Hollinger et al., Proc. Natl. Acad. Sci. USA, 90: 6444-6448 (1993)); Linear antibodies U.S. Pat. No. 5,641,870, “Low pH hydrophobic interaction chromatography for antibody purification” Zapata et al., 1995, “Engineering linear F(ab′)2 fragments for efficient production in Escherichia coli and enhanced antiproliferative activity,” Protein Eng. 8(10): 1057-1062 Nanobodies U.S. Pat. App. Pub. No. 2007/0178082 and Single-domain antibodies (e.g., 2009/0238829, “Stabilized single domain shark IgNAR or VNAR, camelid) antibodies” Heterospecific antibodies U.S. Pat. App. Pub. No. 2006/0149041 and Trivalent antibodies 2006/0149041 “Therapeutic polypeptides, homologues thereof, fragments thereof and for use in modulating platelet-mediated aggregation” U.S. Pat. App. Pub. No. 2009/0252681 “Nanobodies and Polypeptides Against EGFR and IGF-IR” U.S. Pat. App. Pub. No. 2009/0074770, “Amino acid sequences that bind to serum proteins in a manner that is essentially independent of the pH, compounds comprising the same, and uses thereof” U.S. Pat. App. Pub. No. 2009/0028880, “Serum albumin binding proteins” U.S. Pat. App. Pub. No. 2009/0022721, 2007/0077249, and 2007/0237769 “Single domain antibodies directed against tumour necrosis factor-alpha and uses therefor” U.S. Pat. App. Pub. No. 2008/0267949 “Peptides capable of binding to serum proteins” U.S. Pat. App. Pub. No. 2008/0107601 “Nanobodies Against Amyloid-Beta and Polypeptides Comprising the Same for the Treatment of Degenerative Neural Diseases Such as Alzheimer's Disease” U.S. Pat. App. Pub. No. 2008/0096223 “Methods And Assays For Distinguishing Between Different Forms Of Diseases And Disorders Characterized By Thrombocytopenia And/Or By Spontaneous Interaction Between Von Willebrand Factor (Vwf) And Platelets” U.S. Pat. App. Pub. No. 2007/0269422 “Serum albumin binding proteins with long half-lives” U.S. Pat. App. Pub. No. 2006/0246477 and 2006/0211088 “Method for generating variable domain sequences of heavy chain antibodies” U.S. Pat. App. Pub. No. 2006/0115470 “Camelidae antibodies against immunoglobulin e and use thereof for the treatment of allergic disorders” Wesolowski, et al., 2009, “Single domain antibodies: promising experimental and therapeutic tools in infection and immunity,” Med Microbiol Immunol. 198(3): 157-174 US Pat. App. Pub. No. 2009/0148438, “Binding Moieties Based on Shark Ignar Domains” BiTE molecules U.S. Pat. No. 7,235,641, “Bispecific antibodies” U.S. Pat. No. 7,575,923 and 7,112,324, “CD19xCD3 specific polypeptides and uses thereof” US Pat. App. Pub. No. 2006/0193852 “Novel CD19xCD3 specific polypeptides and uses thereof” US Pat. App. Pub. No. 2007/0123479 “Pharmaceutical compositions comprising bispecific anti-cd3, anti-cd19 antibody constructs for the treatment of b-cell related disorders” US Pat. App. Pub. Nos. 2009/0226444 and 2009/0226432, “Pharmaceutical Antibody Compositions with Resistance To Soluble CEA” Domain antibodies (dAbs) U.S. Pat. No. 7,563,443, “Monovalent anti-CD40L antibody polypeptides and compositions thereof” US Pat. App. Pub. No. 2006/0062784 “Compositions monovalent for CD40L binding and methods of use” scFV GenBank Acc. No. CAA12399.1 Anti-beta-galactosidase GenBank Acc. No. CAA12398 Humanized/Modified antibodies U.S. Pat. App. Pub. No. 2009/0191186, “Antibodies to the PcrV Antigen of Pseudomonas aeruginosa” Bebbington, et al., 2008, “Antibodies for the treatment of bacterial infections: current experience and fugure prospects,” Current Opin. in Biotech. 19(6): 613-619 Growth Activin A (Inhibin A) Swiss-Prot Acc. No. P08476.2 (Inhibin beta Factors/Hormones A chain/Activin beta-A chain) US 575751, “Activin-A mutants” Epidermal growth factor (EGF) Swiss-Prot Acc. No. P01133.2 (mature form aa 971-1023) Erythropoietin Swiss-Prot Acc. No. P01588 (mature form aa 28-193) U.S. Pat. No. 7,553,941, “Long-acting polypeptides and methods of producing same” Fibroblast growth factors 1, 2, 21 GenBank Acc. No. NP_061986 (FGF-1, 2, 21) U.S. Pat. No. 7,459,540, “Fibroblast growth factor- like polypeptides” U.S. Pat. No. 7,576,190, “FGF-21 fusion proteins” U.S. Pat. No. 7,491,697, “Muteins of fibroblast growth factor 21” U.S. Pat. No. 7,582,607, “Muteins of fibroblast growth factor 21” GenBank Acc. Nos. AAH18404 and ABI75345 Granulocyte Colony Stimulating GenBank Acc. No. ABI85510.1 Factor U.S. Pat. No. 7,381,804, “G-CSF analog compositions and methods” Growth Hormone GenBank NP_000506.2 Cytoplasmic (mature form aa 27-217) Secreted U.S. Pat. No. 7,553,941, “Long-acting polypeptides Variants and methods of producing same” U.S. Pat. No. 7,553,940, “Long-acting EPO polypeptides and derivatives thereof and methods thereof” Hepatocyte growth factor (HGF) GenBank Acc. No. BAA14348 Keratinocyte growth factor (KGF) Leukemia Inhibitory Factor GenBank Acc. No. AAA51699 (mature form aa 25-213) U.S. Pat. No. 7,445,772, “Heterodimeric four helix bundle cytokines” Nerve growth factor (NGF) Platelet derived growth factor (PDGF) Thrombopoietin Swiss-Prot Acc. No. P40225 (amino acids 22-353) U.S. Pat. No. 6,673,580, “Identification and modification of immunodominant epitopes in polypeptides” Transforming growth factor-alpha (TGF-alpha) Transforming growth factor-beta (TGF-beta) Vascular endothelial growth factor GenBank Acc. No. CAA44447 (VEGF) U.S. Pat. No. 7,427,596, “Variants of vascular endothelial cell growth factor, their uses, and processes for their production” U.S. Pat. No. 7,566,566, “Materials and methods involving hybrid vascular endothelial growth factor DNAs and proteins” Human Therapeutic ApoA1 and ApoA1 Milano GenBank Acc. No. CAT02154 Proteins GenBank Acc. No. ACK12192 U.S. Pat. No. 7,439,323, “Cysteine-containing peptides having antioxidant properties” WO 2008/017906 (mature form aa 25-267) Insulin Swiss-Prot Acc. No. P01308 Proinsulin U.S. Pat. No. 7,547,821, “Methods for the production of insulin in plants” Insulin-like Growth Factor Swiss-Prot. Acc. No. P01343 (IA) U.S. Pat. No. 7,439,063, “Neuroprotective synergy of erythropoietin and insulin-like growth factors” Swiss-Prot. Acc. No. P05019 (IB) U.S. Pat. No. 7,217,796, “Neutralizing human anti- IGFR antibody” Kringle Domains of Human GenBank Acc. No. AAA36451 Plasminogen (amino acids 469-562) U.S. Pat. No. 7,175,840, “Compositions for gene therapy of rheumatoid arthritis including a gene encoding an anti-angiogenic protein or parts thereof” US Pat. App. Pub. No. 2004/0138127, “Novel antiangiogenic peptides, polypeptides encoding same and methods for inhibiting angiogenesis” Chaperones Hsp 90 (human) Swiss-Prot Acc. No. P07900 BiP (human) GRP94 (human) GRP170 (human) Calnexin (human) Calreticulin (human) HSP47 (human) ERp29 (human) Protein disulfide isomerase (PDI) (human) Peptidyl prolyl cis-trans-isomerase (PPI) (human) ERp57 (human) Fusion Proteins/ Ontak (Eisai) Foss, FM, 2001, “Interleukin-2 fusion toxin: Non-natural Proteins targeted therapy for cutaneous T cell lymphoma,” Ann N Y Acad Sci. 941: 166-76. Etanercept (Enbrel) Anthrax rPA fusions U.S. Pat. No. 7,537,771, “Expression system” Therapeutic Nucleoside deaminase GenBank Acc. No. NP_000013.2 Enzymes Antimicrobial glycosidase- GenBank Acc. No. AAB53783 lysostaphin (aa 249-493) Bovine aprotinin U.S. Pat. No. 5,621,074, “Aprotinin analogs” Butyrylcholine esterase GenBank Acc. No. AAA98113.1 U.S. Pat. No. 6,291,175, “Methods for treating a neurological disease by determining BCHE genotype” Ornithine carbamoyltransferase Streptokinase C GenBank Acc. No. P00779 Biocatalytic Carboxylic acid reductase U.S. Pat. No. 5,795,759, “Carboxylic acid reductase, Enzymes (Nocardia) and methods of using same” DszA U.S. Pat. No. 6,071,738, “Conversion of organosulfur DszB compounds to oxyorganosulfur compounds DszC for desulfurization of fossil fuels” DszD U.S. Pat. No. 5,952,208, “Dsz gene expression in (Rhodococcus) pseudomonas hosts” L-aminoacylase Toogood, et al., 2002, “A thermostable L- (Thermococcus litoralis) aminoacylase from Thermococcus litoralis: cloning, overexpression, characterization, and applications in biotransformations,” Extremophiles 6(2): 1431-0651 Singleton, et al., 2000, “Cloning, expression, and characterization of pyrrolidone carboxyl peptidase from the archaeon Thermococcus litoralis” Extremophiles 4 (5), 297-303 Pathogen Chlamydia trachomatis major outer GenBank Acc. No. ABB51004 Proteins/Antigens membrane protein (MOMP) (mature form aa 23-393) Cowpea Chlorotic Mottle Virus coat GenBank Acc. No. NP_613277 protein US Pat. App. Pub. No. 2005/0214321, “Recombinant icosahedral virus like particle production in pseudomonads” Salmonella flagellin and variants GenBank Acc. No. AAA27067 thereof (Salmonella enterica subsp. enterica serovar Typhi) GenBank Acc. No. AAL20871 (Salmonella enterica subsp. enterica serovar Typhimurium str. LT2) US 2007/0224205, “Compositions that include hemagglutinin, methods of making and methods of use thereof” HIV Gag GenBank Acc. No. AAB50258.1 (HIV-1 Gag) HIV Vpr Swiss-Prot Acc. No. P12520.2 HIV Nef GenBank Acc. No. AAA44993 (HIV-1 Nef) Influenza Hemagglutinin GenBank Acc. No. ABW06108.1 (Influenza A HA) P. falciparum circumsporozoite GenBank Acc. No. CAB38998 protein Reagent Proteins, Alpha-1-anti-trypsin U.S. Pat. No. 5,399,684, “DNA sequences expressing Other Proteins mammalian alpha-1-antitrypsin” U.S. Pat. No. 5,736,379, “DNA sequences expressing mammalian alpha₁ antitrypsin” Horseradish Peroxidase C GenBank Acc. No. CAA00083 LRP6 sub-domains Swiss-Prot Acc. No. O75581 (amino acids 20-1370 and subdomians thereof) U.S. Pat. No. 7,416,849, “HBM variants that modulate bone mass and lipid levels” Protein A, Cysteinyl Protein A U.S. Pat. No. 5,151,350, “Cloned genes encoding recombinant protein A” U.S. Pat. No. 5,084,559, “Protein A domain mutants” Streptavidin GenBank Acc. No. CAA00084

In embodiments of the present invention, expression systems that successfully overexpress toxin proteins are identified. Toxin proteins contemplated for expression include, but are not limited to, animal toxins, plant toxins, fungal toxins, and bacterial toxins. Toxin proteins frequently contain structural elements, for example disulfide bonds, that lead to misfolding and insolubility in overexpression efforts. Kunitz-type toxins (KTTs), found in the venom of animals including spiders, snakes, cone snails, and sea anemones, usually have a peptide chain of around 60 amino acids and are stabilized by three disulfide bridges. Botrocetin, a toxin from snake venom that causes platelet aggregation by inducing binding of von Willebrand factor (vWF) to platelet glycoprotein Ib (GPIb), is present in a two-chain form containing both intrachain and interchain disulfide bonds. The Botrocetin two-chain form was reported to be about thirty times more active than the single chain form (Usami, et al., 1993). Catrocollastatin C, a snake venom toxin that impairs platelet aggregation by inhibiting fibrinogen binding to the αIIbβ3 integrin, contains 28 cysteine residues that form 14 disulfide bonds (Calvete, et al., 2000).

Toxin-like proteins have been identified in non-venomous contexts and shown to act as cell activity modulators. Toxin-like proteins include proteases, protease inhibitors, cell antigens, growth factors, etc. A toxin classification tool, ClanTox, available from The Sudarsky Center for Computational Biology at The Hebrew University of Jerusalem in Israel (HUJI) on the HUJI website, predicts whether a given protein is a toxin or toxin-like protein. The server also provides other information, including the presence of a signal peptide, the number of cysteine residues, and associated functional annotations. The tool is described by Naamati, et al., 2009, “ClanTox: a classifier of short animal toxins,” Nucleic Acids Research 37, Web Server issue W363-W368 doi:10.1093/nar/gkp299.

Embodiments of the present invention contemplate the expression of antibodies or antibody fragments. Many forms of antibody fragments are known in the art and encompassed herein. “Antibody fragments” comprise only a portion of an intact antibody, generally including an antigen binding site of the intact antibody and thus retaining the ability to bind antigen. Examples of antibody fragments encompassed by the present definition include: (i) the Fab fragment, having VL, CL, VH and CH1 domains; (ii) the Fab′ fragment, which is a Fab fragment having one or more cysteine residues at the C-terminus of the CH1 domain; (iii) the Fd fragment having VH and CH1 domains; (iv) the Fd′ fragment having VH and CH1 domains and one or more cysteine residues at the C-terminus of the CH1 domain; (v) the Fv fragment having the VL and VH domains of a single arm of an antibody; (vi) the dAb fragment (Ward et al., Nature 341, 544-546 (1989)) which consists of a VH domain; (vii) isolated CDR regions; (viii) F(ab′)₂ fragments, a bivalent fragment including two Fab′ fragments linked by a disulfide bridge at the hinge region; (ix) single chain antibody molecules (e.g., single chain Fv; scFv) (Bird et al., Science 242:423-426 (1988); and Huston et al., PNAS (USA) 85:5879-5883 (1988)); (x) “diabodies” with two antigen binding sites, comprising a heavy chain variable domain (VH) connected to a light chain variable domain (VL) in the same polypeptide chain (see, e.g., EP 404,097; WO 93/11161; and Hollinger et al., Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993)); (xi) “linear antibodies” comprising a pair of tandem Fd segments (VH-CH₁-VH-CH₁) which, together with complementary light chain polypeptides, form a pair of antigen binding regions (Zapata et al. Proteifz Eng. 8(10): 1057-1062 (1995); and U.S. Pat. No. 5,641,870).

Moreover, embodiments of the present invention may include expression of antibody fragments that are modified to improve their stability and or to create antibody complexes with multivalency. For many medical applications, antibody fragments must be sufficiently stable against denaturation or proteolysis conditions, and the antibody fragments should ideally bind the target antigens with high affinity. A variety of techniques and materials have been developed to provide stabilized and or multivalent antibody fragments. An antibody fragment may be fused to a dimerization domain. In one embodiment, the antibody fragments expressed using the compositions and methods of the present invention are dimerized by the attachment of a dimerization domain, such as leucine zippers.

Fusion proteins and other non-natural proteins are also contemplated for expression using the methods and compositions of the invention. A non-natural protein can be, e.g., an engineered protein or a protein obtained by molecular modeling. An example of a fusion protein is Ontak (Eisai Corporation), also called denileukin diftitox or interleukin-2 (IL-2) fusion protein. Ontak was made by replacing the receptor-binding domain of diphtheria toxin with IL-2, the receptor for which is overexpressed in leukemia cells. IL-2 acts to carry the protein inhibitory function of diphtheria toxin to the targeted leukemia cells. Another fusion, Etanercept (Enbrel), links the human gene for soluble TNF receptor 2 to the gene for the Fc component of human immunoglobulin G1.

It is understood that the compositions and methods of the invention can be used to express variants and mutants of the proteins listed herein, regardless of whether specifically noted. Furthermore, as previously described, sequence information required for molecular genetics and genetic engineering techniques relating to many known proteins is widely available, e.g., from GenBank or other sources known to those of skill in the art. The GenBank data herein are provided by way of example. It is understood that if a GenBank accession number is not expressly provided herein, one of skill in the art can identify a desired gene or protein sequence by searching the GenBank database or the published literature.

It is generally recognized that a search of the GenBank database for a particular protein or gene can yield multiple hits. This can be due, e.g., to multiple listings of the same sequence, the occurrence of analogous genes or proteins in different species, or to the listing of truncated, partial, or variant sequences. One knowledgeable in the art will be aware that information relating to the sequence entry is provided in the accompanying information within the record, for example, in a published report cited in the record. Therefore, one of skill in the art, when searching for a sequence to use in the methods and compositions of the invention, will be able to identify the desired sequence from among a list of multiple results.

It is common knowledge in the art that proteins can be functionally equivalent despite differences in amino acid sequence. Substitution of an amino acid by a different amino acid having similar chemical properties and size (e.g., a conservative substitution) often does not significantly change protein function. Even nonconservative amino acid substitutions can be made with no effect on function, for example, when the change is made in a part of the protein that is not critical for function.

A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain, or similar physicochemical characteristics (e.g., electrostatic, hydrogen bonding, isosteric, hydrophobic features). The amino acids may be naturally occurring or non-natural (unnatural). Families of amino acid residues having similar side chains are known in the art. These families include amino acids with basic side chains (e.g. lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, methionine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Substitutions may also include non-conservative changes. Substitutions may also include changes that result in an increased resistance to proteolysis, for example, changes that eliminate a protease recognition site in the recombinant protein.

It is also known to one of skill in the art that proteins having the same amino acid sequence can be encoded by different nucleotide sequences due to the redundancy in the genetic code. The present invention thus includes the use of protein sequences that are different from the sequences provided or referenced herein, or available from public sources, but that are functionally equivalent nonetheless. Also included are proteins that have the same amino acid sequences but are encoded by different nucleotide sequences.

Codon usage or codon preference is well known in the art. The selected coding sequence may be modified by altering the genetic code thereof to match that employed by the bacterial host cell, and the codon sequence thereof may be enhanced to better approximate that employed by the host. Genetic code selection and codon frequency enhancement may be performed according to any of the various methods known to one of ordinary skill in the art, e.g., oligonucleotide-directed mutagenesis. Useful on-line InterNet resources to assist in this process include, e.g.: (1) the Codon Usage Database of the Kazusa DNA Research Institute (2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 Japan); and (2) the Genetic Codes tables available from the NCBI Taxonomy database on the NIH website. For example, Pseudomonas species are reported as utilizing Genetic Code Translation Table 11 of the NCBI Taxonomy site, and as exhibiting the codon usage frequency as shown at the Kazusa site.

Equivalence in protein function can be evaluated by any of a number of assays suitable for the particular protein, as known in the art and described elsewhere herein. For example, the function of an antibody can be evaluated by measuring its binding to its target antigen, and enzymes can be evaluated by activity assay.

Host Cell

In one embodiment the invention provides an array of P. fluorescens host cells from which to optimally produce a heterologous protein or peptide of interest. P. fluorescens has been demonstrated to be an improved platform for production of a variety of proteins and several efficient secretion signals have been identified from this organism (see, e.g., U.S. Pat. App. Pub. No. 2006/0008877 and 2008/0193974).

The Pseudomonads system offers advantages for commercial expression of polypeptides and enzymes, in comparison with other bacterial expression systems. In particular, P. fluorescens has been identified as an advantageous expression system. P. fluorescens encompasses a group of common, nonpathogenic saprophytes that colonize soil, water and plant surface environments. Commercial enzymes derived from P. fluorescens have been used to reduce environmental contamination, as detergent additives, and for stereoselective hydrolysis. P. fluorescens is also used agriculturally to control pathogens. U.S. Pat. No. 4,695,462 describes the expression of recombinant bacterial proteins in P. fluorescens.

It is contemplated that alternate host cells, particularly E. coli, which utilizes expression elements described herein in a manner similar to P. fluorescens, or a multiplicity of different host cells, can be used to generate an array comprising a plurality of phenotypically distinct host cells that have been genetically modified to modulate the expression of one or more target genes, as discussed supra. The host cell can be any organism in which target genes can be altered. Methods of identifying target genes homologous to those listed in Tables 1 and 2 are known in the art. Further, one of skill in the art would understand how to identify target genes that are native to or useful in a host cell of interest. Many of these proteins are well known in the art. See, for example, U.S. Patent Application Publication No. 2006/0110747).

Host cells can be selected from “Gram-negative Proteobacteria Subgroup 18.” “Gram-negative Proteobacteria Subgroup 18” is defined as the group of all subspecies, varieties, strains, and other sub-special units of the species Pseudomonas fluorescens, including those belonging, e.g., to the following (with the ATCC or other deposit numbers of exemplary strain(s) shown in parenthesis): Pseudomonas fluorescens biotype A, also called biovar 1 or biovar I (ATCC 13525); Pseudomonas fluorescens biotype B, also called biovar 2 or biovar II (ATCC 17816); Pseudomonas fluorescens biotype C, also called biovar 3 or biovar III (ATCC 17400); Pseudomonas fluorescens biotype F, also called biovar 4 or biovar IV (ATCC 12983); Pseudomonas fluorescens biotype G, also called biovar 5 or biovar V (ATCC 17518); Pseudomonas fluorescens biovar VI; Pseudomonas fluorescens Pf0-1; Pseudomonas fluorescens Pf-5 (ATCC BAA-477); Pseudomonas fluorescens SBW25; and Pseudomonas fluorescens subsp. cellulosa (NCIMB 10462).

The host cell can be selected from “Gram-negative Proteobacteria Subgroup 19.” “Gram-negative Proteobacteria Subgroup 19” is defined as the group of all strains of Pseudomonas fluorescens biotype A. A particularly preferred strain of this biotype is P. fluorescens strain MB101 (see U.S. Pat. No. 5,169,760 to Wilcox), and derivatives thereof. An example of a preferred derivative thereof is P. fluorescens strain MB214, constructed by inserting into the MB101 chromosomal asd (aspartate dehydrogenase gene) locus, a native E. coli PlacI-lacI-lacZYA construct (i.e. in which PlacZ was deleted).

Additional P. fluorescens strains that can be used in the present invention include Pseudomonas fluorescens Migula and Pseudomonas fluorescens Loitokitok, having the following ATCC designations: [NCIB 8286]; NRRL B-1244; NCIB 8865 strain CO1; NCIB 8866 strain CO2; 1291 [ATCC 17458; IFO 15837; NCIB 8917; LA; NRRL B-1864; pyrrolidine; PW2 [ICMP 3966; NCPPB 967; NRRL B-899]; 13475; NCTC 10038; NRRL B-1603 [6; IFO 15840]; 52-1C; CCEB 488-A [BU 140]; CCEB 553 [EM 15/47]; IAM 1008 [AHH-27]; IAM 1055 [AHH-23]; 1 [IFO 15842]; 12 [ATCC 25323; NIH 11; den Dooren de Jong 216]; 18 [IFO 15833; WRRL P-7]; 93 [TR-10]; 108 [52-22; IFO 15832]; 143 [IFO 15836; PL]; 149 [2-40-40; IFO 15838]; 182 [IFO 3081; PJ 73]; 184 [IFO 15830]; 185 [W2 L-1]; 186 [IFO 15829; PJ 79]; 187 [NCPPB 263]; 188 [NCPPB 316]; 189 [PJ227; 1208]; 191 [IFO 15834; PJ 236; 22/1]; 194 [Klinge R-60; PJ 253]; 196 [PJ 288]; 197 [PJ 290]; 198 [PJ 302]; 201 [PJ 368]; 202 [PJ 372]; 203 [PJ 376]; 204 [IFO 15835; PJ 682]; 205 [PJ 686]; 206 [PJ 692]; 207 [PJ 693]; 208 [PJ 722]; 212. [PJ 832]; 215 [PJ 849]; 216 [PJ 885]; 267 [B-9]; 271 [B-1612]; 401 [C71A; IFO 15831; PJ 187]; NRRL B-3178 [4; IFO. 15841]; KY 8521; 3081; 30-21; [IFO 3081]; N; PYR; PW; D946-B83 [BU 2183; FERM-P 3328]; P-2563 [FERM-P 2894; IFO 13658]; IAM-1126 [43F]; M-1; A506 [A5-06]; A505 [A5-05-1]; A526 [A5-26]; B69; 72; NRRL B-4290; PMW6 [NCIB 11615]; SC 12936; A1 [IFO 15839]; F 1847 [CDC-EB]; F 1848 [CDC 93]; NCIB 10586; P17; F-12; AmMS 257; PRA25; 6133D02; 6519E01; Ni; SC15208; BNL-WVC; NCTC 2583 [NCIB 8194]; H13; 1013 [ATCC 11251; CCEB 295]; IFO 3903; 1062; or Pf-5.

In one embodiment, the host cell can be any cell capable of producing a protein or polypeptide of interest, including a P. fluorescens cell as described above. The most commonly used systems to produce proteins or polypeptides of interest include certain bacterial cells, particularly E. coli, because of their relatively inexpensive growth requirements and potential capacity to produce protein in large batch cultures. Yeasts are also used to express biologically relevant proteins and polypeptides, particularly for research purposes. Systems include Saccharomyces cerevisiae or Pichia pastoris. These systems are well characterized, provide generally acceptable levels of total protein production and are comparatively fast and inexpensive. Insect cell expression systems have also emerged as an alternative for expressing recombinant proteins in biologically active form. In some cases, correctly folded proteins that are post-translationally modified can be produced. Mammalian cell expression systems, such as Chinese hamster ovary cells, have also been used for the expression of proteins or polypeptides of interest. On a small scale, these expression systems are often effective. Certain biologics can be derived from proteins, particularly in animal or human health applications. In another embodiment, the host cell is a plant cell, including, but not limited to, a tobacco cell, corn, a cell from an Arabidopsis species, potato or rice cell.

In another embodiment, the host cell can be a prokaryotic cell such as a bacterial cell including, but not limited to, an Escherichia or a Pseudomonas species. Typical bacterial cells are described, for example, in “Biological Diversity: Bacteria and Archaeans,” a chapter of the On-Line Biology Book, provided by Dr. M. J. Farabee of the Estrella Mountain Community College, Arizona, USA. In certain embodiments, the host cell can be a Pseudomonad cell, and can typically be a P. fluorescens cell. In other embodiments, the host cell can also be an E. coli cell. In another embodiment the host cell can be a eukaryotic cell, for example an insect cell, including but not limited to a cell from a Spodoptera, Trichoplusia, Drosophila or an Estigmene species, or a mammalian cell, including but not limited to a murine cell, a hamster cell, a monkey cell, a primate cell or a human cell.

In one embodiment, the host cell can be a member of any of the bacterial taxa. The cell can, for example, be a member of any species of eubacteria. The host can be a member of any one of the taxa: Acidobacteria, Actinobacteira, Aquificae, Bacteroidetes, Chlorobi, Chlamydiae, Choroflexi, Chrysiogenetes, Cyanobacteria, Deferribacteres, Deinococcus, Dictyoglomi, Fibrobacteres, Firmicutes, Fusobacteria, Gemmatimonadetes, Lentisphaerae, Nitrospirae, Planctomycetes, Proteobacteria, Spirochaetes, Thermodesulfobacteria, Thermomicrobia, Thermotogae, Thermus (Thermales), or Verrucomicrobia. In an embodiment of a eubacterial host cell, the cell can be a member of any species of eubacteria, excluding Cyanobacteria.

The bacterial host can also be a member of any species of Proteobacteria. A proteobacterial host cell can be a member of any one of the taxa Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, or Epsilonproteobacteria. In addition, the host can be a member of any one of the taxa Alphaproteobacteria, Betaproteobacteria, or Gammaproteobacteria, and a member of any species of Gammaproteobacteria.

In one embodiment of a Gamma Proteobacterial host, the host will be member of any one of the taxa Aeromonadales, Alteromonadales, Enterobacteriales, Pseudomonad ales, or Xanthomonadales; or a member of any species of the Enterobacteriales or Pseudomonad ales. In one embodiment, the host cell can be of the order Enterobacteriales, the host cell will be a member of the family Enterobacteriaceae, or may be a member of any one of the genera Erwinia, Escherichia, or Serratia; or a member of the genus Escherichia. Where the host cell is of the order Pseudomonad ales, the host cell may be a member of the family Pseudomonadaceae, including the genus Pseudomonas. Gamma Proteobacterial hosts include members of the species Escherichia coli and members of the species Pseudomonas fluorescens.

Other Pseudomonas organisms may also be useful. Pseudomonads and closely related species include Gram-negative Proteobacteria Subgroup 1, which include the group of Proteobacteria belonging to the families and/or genera described as “Gram-Negative Aerobic Rods and Cocci” by R. E. Buchanan and N. E. Gibbons (eds.), Bergey's Manual of Determinative Bacteriology, pp. 217-289 (8th ed., 1974) (The Williams & Wilkins Co., Baltimore, Md., USA) (hereinafter “Bergey (1974)”). Table 10 presents these families and genera of organisms.

TABLE 10 Families and Genera Listed in the Part, “Gram-Negative Aerobic Rods and Cocci” (in Bergey (1974)) Family I. Pseudomonaceae Gluconobacter Pseudomonas Xanthomonas Zoogloea Family II. Azotobacteraceae Azomonas Azotobacter Beijerinckia Derxia Family III. Rhizobiaceae Agrobacterium Rhizobium Family IV. Methylomonadaceae Methylococcus Methylomonas Family V. Halobacteriaceae Halobacterium Halococcus Other Genera Acetobacter Alcaligenes Bordetella Brucella Francisella Thermus

“Gram-negative Proteobacteria Subgroup 1” also includes Proteobacteria that would be classified in this heading according to the criteria used in the classification. The heading also includes groups that were previously classified in this section but are no longer, such as the genera Acidovorax, Brevundimonas, Burkholderia, Hydrogenophaga, Oceanimonas, Ralstonia, and Stenotrophomonas, the genus Sphingomonas (and the genus Blastomonas, derived therefrom), which was created by regrouping organisms belonging to (and previously called species of) the genus Xanthomonas, the genus Acidomonas, which was created by regrouping organisms belonging to the genus Acetobacter as defined in Bergey (1974). In addition hosts can include cells from the genus Pseudomonas, Pseudomonas enalia (ATCC 14393), Pseudomonas nigrifaciensi (ATCC 19375), and Pseudomonas putrefaciens (ATCC 8071), which have been reclassified respectively as Alteromonas haloplanktis, Alteromonas nigrifaciens, and Alteromonas putrefaciens. Similarly, e.g., Pseudomonas acidovorans (ATCC 15668) and Pseudomonas testosteroni (ATCC 11996) have since been reclassified as Comamonas acidovorans and Comamonas testosteroni, respectively; and Pseudomonas nigrifaciens (ATCC 19375) and Pseudomonas piscicida (ATCC 15057) have been reclassified respectively as Pseudoalteromonas nigrifaciens and Pseudoalteromonas piscicida. “Gram-negative Proteobacteria Subgroup 1” also includes Proteobacteria classified as belonging to any of the families: Pseudomonad aceae, Azotobacteraceae (now often called by the synonym, the “Azotobacter group” of Pseudomonad aceae), Rhizobiaceae, and Methylomonadaceae (now often called by the synonym, “Methylococcaceae”). Consequently, in addition to those genera otherwise described herein, further Proteobacterial genera falling within “Gram-negative Proteobacteria Subgroup 1” include: 1) Azotobacter group bacteria of the genus Azorhizophilus; 2) Pseudomonad aceae family bacteria of the genera Cellvibrio, Oligella, and Teredinibacter; 3) Rhizobiaceae family bacteria of the genera Chelatobacter, Ensifer, Liberibacter (also called “Candidatus Liberibacter”), and Sinorhizobium; and 4) Methylococcaceae family bacteria of the genera Methylobacter, Methylocaldum, Methylomicrobium, Methylosarcina, and Methylosphaera.

In another embodiment, the host cell is selected from “Gram-negative Proteobacteria Subgroup 2.” “Gram-negative Proteobacteria Subgroup 2” is defined as the group of Proteobacteria of the following genera (with the total numbers of catalog-listed, publicly-available, deposited strains thereof indicated in parenthesis, all deposited at ATCC, except as otherwise indicated): Acidomonas (2); Acetobacter (93); Gluconobacter (37); Brevundimonas (23); Beyerinckia (13); Derxia (2); Brucella (4); Agrobacterium (79); Chelatobacter (2); Ensifer (3); Rhizobium (144); Sinorhizobium (24); Blastomonas (1); Sphingomonas (27); Alcaligenes (88); Bordetella (43); Burkholderia (73); Ralstonia (33); Acidovorax (20); Hydrogenophaga (9); Zoogloea (9); Methylobacter (2); Methylocaldum (1 at NCIMB); Methylococcus (2); Methylomicrobium (2); Methylomonas (9); Methylosarcina (1); Methylosphaera; Azomonas (9); Azorhizophilus (5); Azotobacter (64); Cellvibrio (3); Oligella (5); Pseudomonas (1139); Francisella (4); Xanthomonas (229); Stenotrophomonas (50); and Oceanimonas (4).

Exemplary host cell species of “Gram-negative Proteobacteria Subgroup 2” include, but are not limited to the following bacteria (with the ATCC or other deposit numbers of exemplary strain(s) thereof shown in parenthesis): Acidomonas methanolica (ATCC 43581); Acetobacter aceti (ATCC 15973); Gluconobacter oxydans (ATCC 19357); Brevundimonas diminuta (ATCC 11568); Beijerinckia indica (ATCC 9039 and ATCC 19361); Derxia gummosa (ATCC 15994); Brucella melitensis (ATCC 23456), Brucella abortus (ATCC 23448); Agrobacterium tumefaciens (ATCC 23308), Agrobacterium radiobacter (ATCC 19358), Agrobacterium rhizogenes (ATCC 11325); Chelatobacter heintzii (ATCC 29600); Ensifer adhaerens (ATCC 33212); Rhizobium leguminosarum (ATCC 10004); Sinorhizobium fredii (ATCC 35423); Blastomonas natatoria (ATCC 35951); Sphingomonas paucimobilis (ATCC 29837); Alcaligenes faecalis (ATCC 8750); Bordetella pertussis (ATCC 9797); Burkholderia cepacia (ATCC 25416); Ralstonia pickettii (ATCC 27511); Acidovorax facilis (ATCC 11228); Hydrogenophagaflava (ATCC 33667); Zoogloea ramigera (ATCC 19544); Methylobacter luteus (ATCC 49878); Methylocaldum gracile (NCIMB 11912); Methylococcus capsulatus (ATCC 19069); Methylomicrobium agile (ATCC 35068); Methylomonas methanica (ATCC 35067); Methylosarcina fibrata (ATCC 700909); Methylosphaera hansonii (ACAM 549); Azomonas agilis (ATCC 7494); Azorhizophilus paspali (ATCC 23833); Azotobacter chroococcum (ATCC 9043); Cellvibrio mixtus (UQM 2601); Oligella urethralis (ATCC 17960); Pseudomonas aeruginosa (ATCC 10145), Pseudomonas fluorescens (ATCC 35858); Francisella tularensis (ATCC 6223); Stenotrophomonas maltophilia (ATCC 13637); Xanthomonas campestris (ATCC 33913); and Oceanimonas doudoroffli (ATCC 27123).

In another embodiment, the host cell is selected from “Gram-negative Proteobacteria Subgroup 3.” “Gram-negative Proteobacteria Subgroup 3” is defined as the group of Proteobacteria of the following genera: Brevundimonas; Agrobacterium; Rhizobium; Sinorhizobium; Blastomonas; Sphingomonas; Alcaligenes; Burkholderia; Ralstonia; Acidovorax; Hydrogenophaga; Methylobacter; Methylocaldum; Methylococcus; Methylomicrobium; Methylomonas; Methylosarcina; Methylosphaera; Azomonas; Azorhizophilus; Azotobacter Cellvibrio; Oligella; Pseudomonas; Teredinibacter; Francisella; Stenotrophomonas; Xanthomonas; and Oceanimonas.

In another embodiment, the host cell is selected from “Gram-negative Proteobacteria Subgroup 4.” “Gram-negative Proteobacteria Subgroup 4” is defined as the group of Proteobacteria of the following genera: Brevundimonas; Blastomonas; Sphingomonas; Burkholderia; Ralstonia; Acidovorax; Hydrogenophaga; Methylobacter; Methylocaldum; Methylococcus; Methylomicrobium; Methylomonas; Methylosarcina; Methylosphaera; Azomonas; Azorhizophilus; Azotobacter; Cellvibrio; Oligella; Pseudomonas; Teredinibacter; Francisella; Stenotrophomonas; Xanthomonas; and Oceanimonas.

In another embodiment, the host cell is selected from “Gram-negative Proteobacteria Subgroup 5.” “Gram-negative Proteobacteria Subgroup 5” is defined as the group of Proteobacteria of the following genera: Methylobacter; Methylocaldum; Methylococcus; Methylomicrobium; Methylomonas; Methylosarcina; Methylosphaera; Azomonas; Azorhizophilus; Azotobacter; Cellvibrio; Oligella; Pseudomonas; Teredinibacter; Francisella; Stenotrophomonas; Xanthomonas; and Oceanimonas.

The host cell can be selected from “Gram-negative Proteobacteria Subgroup 6.” “Gram-negative Proteobacteria Subgroup 6” is defined as the group of Proteobacteria of the following genera: Brevundimonas; Blastomonas; Sphingomonas; Burkholderia; Ralstonia; Acidovorax; Hydrogenophaga; Azomonas; Azorhizophilus; Azotobacter; Cellvibrio; Oligella; Pseudomonas; Teredinibacter; Stenotrophomonas; Xanthomonas; and Oceanimonas.

The host cell can be selected from “Gram-negative Proteobacteria Subgroup 7.” “Gram-negative Proteobacteria Subgroup 7” is defined as the group of Proteobacteria of the following genera: Azomonas; Azorhizophilus; Azotobacter; Cellvibrio; Oligella; Pseudomonas; Teredinibacter; Stenotrophomonas; Xanthomonas; and Oceanimonas.

The host cell can be selected from “Gram-negative Proteobacteria Subgroup 8.” “Gram-negative Proteobacteria Subgroup 8” is defined as the group of Proteobacteria of the following genera: Brevundimonas; Blastomonas; Sphingomonas; Burkholderia; Ralstonia; Acidovorax; Hydrogenophaga; Pseudomonas; Stenotrophomonas; Xanthomonas; and Oceanimonas.

The host cell can be selected from “Gram-negative Proteobacteria Subgroup 9.” “Gram-negative Proteobacteria Subgroup 9” is defined as the group of Proteobacteria of the following genera: Brevundimonas; Burkholderia; Ralstonia; Acidovorax; Hydrogenophaga; Pseudomonas; Stenotrophomonas; and Oceanimonas.

The host cell can be selected from “Gram-negative Proteobacteria Subgroup 10.” “Gram-negative Proteobacteria Subgroup 10” is defined as the group of Proteobacteria of the following genera: Burkholderia; Ralstonia; Pseudomonas; Stenotrophomonas; and Xanthomonas.

The host cell can be selected from “Gram-negative Proteobacteria Subgroup 11.” “Gram-negative Proteobacteria Subgroup 11” is defined as the group of Proteobacteria of the genera: Pseudomonas; Stenotrophomonas; and Xanthomonas. The host cell can be selected from “Gram-negative Proteobacteria Subgroup 12.” “Gram-negative Proteobacteria Subgroup 12” is defined as the group of Proteobacteria of the following genera: Burkholderia; Ralstonia; Pseudomonas. The host cell can be selected from “Gram-negative Proteobacteria Subgroup 13.” “Gram-negative Proteobacteria Subgroup 13” is defined as the group of Proteobacteria of the following genera: Burkholderia; Ralstonia; Pseudomonas; and Xanthomonas. The host cell can be selected from “Gram-negative Proteobacteria Subgroup 14.” “Gram-negative Proteobacteria Subgroup 14” is defined as the group of Proteobacteria of the following genera: Pseudomonas and Xanthomonas. The host cell can be selected from “Gram-negative Proteobacteria Subgroup 15.” “Gram-negative Proteobacteria Subgroup 15” is defined as the group of Proteobacteria of the genus Pseudomonas.

The host cell can be selected from “Gram-negative Proteobacteria Subgroup 16.” “Gram-negative Proteobacteria Subgroup 16” is defined as the group of Proteobacteria of the following Pseudomonas species (with the ATCC or other deposit numbers of exemplary strain(s) shown in parenthesis): Pseudomonas abietaniphila (ATCC 700689); Pseudomonas aeruginosa (ATCC 10145); Pseudomonas alcaligenes (ATCC 14909); Pseudomonas anguilliseptica (ATCC 33660); Pseudomonas citronellolis (ATCC 13674); Pseudomonas flavescens (ATCC 51555); Pseudomonas mendocina (ATCC 25411); Pseudomonas nitroreducens (ATCC 33634); Pseudomonas oleovorans (ATCC 8062); Pseudomonas pseudoalcaligenes (ATCC 17440); Pseudomonas resinovorans (ATCC 14235); Pseudomonas straminea (ATCC 33636); Pseudomonas agarici (ATCC 25941); Pseudomonas alcaliphila; Pseudomonas alginovora; Pseudomonas andersonii; Pseudomonas asplenii (ATCC 23835); Pseudomonas azelaica (ATCC 27162); Pseudomonas beyerinckii (ATCC 19372); Pseudomonas borealis; Pseudomonas boreopolis (ATCC 33662); Pseudomonas brassicacearum; Pseudomonas butanovora (ATCC 43655); Pseudomonas cellulosa (ATCC 55703); Pseudomonas aurantiaca (ATCC 33663); Pseudomonas chlororaphis (ATCC 9446, ATCC 13985, ATCC 17418, ATCC 17461); Pseudomonas fragi (ATCC 4973); Pseudomonas lundensis (ATCC 49968); Pseudomonas taetrolens (ATCC 4683); Pseudomonas cissicola (ATCC 33616); Pseudomonas coronafaciens; Pseudomonas diterpeniphila; Pseudomonas elongata (ATCC 10144); Pseudomonasflectens (ATCC 12775); Pseudomonas azotoformans; Pseudomonas brenneri; Pseudomonas cedrella; Pseudomonas corrugata (ATCC 29736); Pseudomonas extremorientalis; Pseudomonas fluorescens (ATCC 35858); Pseudomonas gessardii; Pseudomonas libanensis; Pseudomonas mandelii CC 700871); Pseudomonas marginalis CC 10844); Pseudomonas migulae; Pseudomonas mucidolens (ATCC 4685); Pseudomonas orientalis; Pseudomonas rhodesiae; Pseudomonas synxantha (ATCC 9890); Pseudomonas tolaasii (ATCC 33618); Pseudomonas veronii (ATCC 700474); Pseudomonas frederiksbergensis; Pseudomonas geniculata (ATCC 19374); Pseudomonas gingeri; Pseudomonas graminis; Pseudomonas grimontii; Pseudomonas halodenitrificans; Pseudomonas halophila; Pseudomonas hibiscicola (ATCC 19867); Pseudomonas huttiensis (ATCC 14670); Pseudomonas hydrogenovora; Pseudomonas jessenii (ATCC 700870); Pseudomonas kilonensis; Pseudomonas lanceolata (ATCC 14669); Pseudomonas lini; Pseudomonas marginate (ATCC 25417); Pseudomonas mephitica (ATCC 33665); Pseudomonas denitrificans (ATCC 19244); Pseudomonas pertucinogena (ATCC 190); Pseudomonas pictorum (ATCC 23328); Pseudomonas psychrophila; Pseudomonas filva (ATCC 31418); Pseudomonas monteilii (ATCC 700476); Pseudomonas mosselii; Pseudomonas oryzihabitans (ATCC 43272); Pseudomonas plecoglossicida (ATCC 700383); Pseudomonas putida (ATCC 12633); Pseudomonas reactans; Pseudomonas spinosa (ATCC 14606); Pseudomonas balearica; Pseudomonas luteola (ATCC 43273); Pseudomonas stutzeri (ATCC 17588); Pseudomonas amygdali (ATCC 33614); Pseudomonas avellanae (ATCC 700331); Pseudomonas caricapapayae (ATCC 33615); Pseudomonas cichorii (ATCC 10857); Pseudomonas ficuserectae (ATCC 35104); Pseudomonas fuscovaginae; Pseudomonas meliae (ATCC 33050); Pseudomonas syringae (ATCC 19310); Pseudomonas viridiflava (ATCC 13223); Pseudomonas thermocarboxydovorans (ATCC 35961); Pseudomonas thermotolerans; Pseudomonas thivervalensis; Pseudomonas vancouverensis (ATCC 700688); Pseudomonas wisconsinensis; and Pseudomonas xiamenensis.

The host cell can be selected from “Gram-negative Proteobacteria Subgroup 17.” “Gram-negative Proteobacteria Subgroup 17” is defined as the group of Proteobacteria known in the art as the “fluorescent Pseudomonads” including those belonging, e.g., to the following Pseudomonas species: Pseudomonas azotoformans; Pseudomonas brenneri; Pseudomonas cedrella; Pseudomonas corrugata; Pseudomonas extremorientalis; Pseudomonas fluorescens; Pseudomonas gessardii; Pseudomonas libanensis; Pseudomonas mandelii; Pseudomonas marginalis; Pseudomonas migulae; Pseudomonas mucidolens; Pseudomonas orientalis; Pseudomonas rhodesiae; Pseudomonas synxantha; Pseudomonas tolaasii; and Pseudomonas veronii.

Other suitable hosts include those classified in other parts of the reference, such as Gram (+) Proteobacteria. In one embodiment, the host cell is an E. coli. The genome sequence for E. coli has been established for E. coli MG1655 (Blattner, et al. (1997) The complete genome sequence of Escherichia coli K-12, Science 277(5331): 1453-74) and DNA microarrays are available commercially for E. coli K12 (MWG Inc, High Point, N.C.). E. coli can be cultured in either a rich medium such as Luria-Bertani (LB) (10 g/L tryptone, 5 g/L NaCl, 5 g/L yeast extract) or a defined minimal medium such as M9 (6 g/L Na₂HPO₄, 3 g/L KH₂PO₄, 1 g/L NH₄C1, 0.5 g/L NaCl, pH 7.4) with an appropriate carbon source such as 1% glucose. Routinely, an over night culture of E. coli cells is diluted and inoculated into fresh rich or minimal medium in either a shake flask or a fermentor and grown at 37° C.

A host cell can also be of mammalian origin, such as a cell derived from a mammal including any human or non-human mammal. Mammals can include, but are not limited to primates, monkeys, porcine, ovine, bovine, rodents, ungulates, pigs, swine, sheep, lambs, goats, cattle, deer, mules, horses, monkeys, apes, dogs, cats, rats, and mice.

A host cell may also be of plant origin. Cells from any plant can be selected in which to screen for the production of a heterologous protein of interest. Examples of suitable plant include, but are not limited to, alfalfa, apple, apricot, Arabidopsis, artichoke, arugula, asparagus, avocado, banana, barley, beans, beet, blackberry, blueberry, broccoli, brussels sprouts, cabbage, canola, cantaloupe, carrot, cassaya, castorbean, cauliflower, celery, cherry, chicory, cilantro, citrus, clementines, clover, coconut, coffee, corn, cotton, cranberry, cucumber, Douglas fir, eggplant, endive, escarole, eucalyptus, fennel, figs, garlic, gourd, grape, grapefruit, honey dew, jicama, kiwifruit, lettuce, leeks, lemon, lime, Loblolly pine, linseed, mango, melon, mushroom, nectarine, nut, oat, oil palm, oil seed rape, okra, olive, onion, orange, an ornamental plant, palm, papaya, parsley, parsnip, pea, peach, peanut, pear, pepper, persimmon, pine, pineapple, plantain, plum, pomegranate, poplar, potato, pumpkin, quince, radiata pine, radiscchio, radish, rapeseed, raspberry, rice, rye, sorghum, Southern pine, soybean, spinach, squash, strawberry, sugarbeet, sugarcane, sunflower, sweet potato, sweetgum, tangerine, tea, tobacco, tomato, triticale, turf, turnip, a vine, watermelon, wheat, yams, and zucchini. In some embodiments, plants useful in the method are Arabidopsis, corn, wheat, soybean, and cotton.

Kits

The present invention also provides kits useful for identifying a host strain, e.g. a P. fluorescens host strain, optimal for producing a heterologous protein or polypeptide of interest. The kit comprises a plurality of phenotypically distinct host cells, wherein each population has been genetically modified to increase the expression of one or more target genes involved in protein production, to decrease the expression of one or more target genes involved in protein degradation, or both. The array may further comprise one or more populations of cells that have not been genetically modified to modulate the expression of either a gene involved in protein production or a gene involved in protein degradation. These kits may also comprise reagents sufficient to facilitate growth and maintenance of the cell populations as well as reagents and/or constructs for expression of a heterologous protein or polypeptide of interest. The populations of host cells may be provided in the kit in any manner suitable for storage, transport, and reconstitution of cell populations. The cell populations may be provided live in a tube, on a plate, or on a slant, or may be preserved either freeze-dried or frozen in a tube or vial. The cell populations may contain additional components in the storage media such as glycerol, sucrose, albumin, or other suitable protective or storage agents.

The following examples are offered by way of illustration and not by way of limitation.

EXPERIMENTAL EXAMPLES Overview

Heterologous protein production often leads to the formation of insoluble or improperly folded proteins, which are difficult to recover and may be inactive. Furthermore, the presence of specific host cell proteases may degrade the protein of interest and thus reduce the final yield. There is no single factor that will improve the production of all heterologous proteins. Thus, a method was sought to identify factors specific to a particular heterologous protein from a pool of likely candidates.

Using Systems Biology tools, the P. fluorescens genome was mined to identify host cell protein folding modulator and protease genes. Then, global gene expression analyses were performed to prioritize upregulated targets, and, thereafter, novel protein production strains were constructed. As a result, a “Pfēnex Strain Array” was assembled consisting of a plurality of phenotypically distinct P. fluorescens host strains that are deficient in host-cell proteases or allow the co-overexpression of protein folding modulators. This strain array can be used to screen for factors that specifically enhance the yield or quality of certain heterologous proteins. Providing a plurality of phenotypically distinct host strains increases the chance of success of identifying a host strain that will increase the production of any individual heterologous protein of interest.

This invention provides an improvement in the production of heterologous proteins in Pseudomonas fluorescens. Having available a library of host strains in the same genetic background allows the rapid screening and identification of factors that increase the yield and/or quality of heterologously expressed proteins. The genome sequence of P. fluorescens has been annotated and targeted host cell folding modulators and proteases have been identified. Folding modulators assist in the proper folding of proteins and include chaperones, chaperonins, peptidyl-proline isomerases (PPIases), and disulfide bond formation proteins. Proteases can degrade the protein of interest and thus affect heterologous protein yield and quality. Using background knowledge from the literature and DNA microarray analyses to identify likely targets, a list of about 80 target genes was assembled. In host cells that have the same genetic background, these genes were either removed from the genome or cloned into plasmids to enable co-overexpression along with heterologous proteins. The resulting strains were arrayed in 96-well format and, after transformation of plasmids that express the heterologous protein of interest, were screened for improved protein yield and/or quality.

Example 1 Identification of Folding Modulator Genes in the Genome of P. fluorescens Strain MB214

Folding modulators are a class of proteins present in all cells which aid in the folding, unfolding and degradation of nascent and heterologous polypeptides. Folding modulators include chaperones, chaperonins, peptidyl-prolyl cis-trans isomerases, and proteins involved in protein disulfide bond formation. As a first step to construct novel production strains with the ability to help fold heterologous proteins, the P. fluorescens genome was mined to identify host cell folding modulator genes.

Each of the 6,433 predicted ORFs of the P. fluorescens MB214 genome was analyzed for the possibility that they encoded a folding modulator using the following method. Several folding modulators of interest had already been identified by Dow researchers by analysis of the genome annotation (Ramseier et. al. 2001). Homologs of these starting proteins were identified using protein/protein BLAST with the starting protein as the query and a database of all MB214 translated ORFs as the subject. Those translated ORFs which matched the query proteins with significant homology were added to the list for further analysis. Significant homology is defined here as having an e-score of 1e-30 or less with allowances made for human judgment based on the length and quality of the alignment. The intention of this study was to be very inclusive to maximize the chance that all potential folding modulators would be identified.

More ORFs were added to the list based on their curated function from the previous annotation containing the keyword “chaperone”. Finally, the ORFs were analyzed by the protein signature family searching program InterProScan (Quevillon et. al. 2005) against the InterPro Database version 7.0 (Mulder et. al. 2005). The ORFs were assigned protein families by the InterProScan software as well as Gene Ontology (GO) categories associated with those families (Gene Ontology Consortium. 2004). Using these automatic GO assignments, all of the ORFs which had been assigned the GO terms “GO:0006457 Biological Process: protein folding” or “GO:0003754 Molecular Function: chaperone activity” were added to the list for further analysis.

The list was then analyzed to remove ORFs which had a low probability of encoding folding modulators. Again, the intent of this study was to be very inclusive but many of the ORFs assigned to the list by these semi-automated methods could be easily identified as not coding for folding modulators based on limited criteria and human judgment.

The most common reason for excluding a certain ORF was the weak evidence that this ORF is actually a folding modulator, i.e. ORFs which had been assigned to the list based on the previous annotation where the reasoning for annotating the ORF as a folding modulator was either unclear or contradictory. InterProScan is actually a conglomerate of different programs and some of these programs are considered to be more reliable than others. If an ORF was assigned to the list based solely on the output of the ScanRegExp or ProfileScan components then it was removed. The final list of P. fluorescens folding modulators has 43 members and is shown in Table 1.

Example 2 Identification of Protease Genes in the Genome of P. fluorescens Strain MB214

Proteases are enzymes that hydrolyze peptide bonds and are necessary for the survival of all living creatures. However, their role in the cell means that proteases can be detrimental to recombinant protein yield and/or quality in any heterologous protein expression system, which also includes the Pfenex Expression Technology™. As a first step to construct novel production strains that have protease genes removed from the genome, the P. fluorescens genome was mined to identify host cell protease genes.

Each of the 6,433 predicted ORFs of the P. fluorescens MB214 genome were analyzed for the possibility that they encoded a protease using the following method. The MEROPS database is manually curated by researchers at the Wellcome Trust Sanger Institute, Cambridge, UK (Rawlings et. al., 2006, Nucleic Acids Research 34 (Database issue): D270-2. It is a comprehensive list of proteases discovered both through laboratory experiments as well as by homology to known protease families. One of the strengths of the database is the MEROPS hierarchical classification scheme. In this system, homologs which share the same function are grouped together into families. Families are grouped into clans based on evolutionary relatedness that again are based on similar structural characteristics. The method makes great use of the database to identify protease homologs within the P. fluorescens genome.

Homologs to the MEROPS database were identified using protein/protein BLAST with each MB214 translated ORF as the query and a database of all of the MEROPS proteins as the subject. Those translated ORFs, which matched the query proteins with significant homology, were added to the list for further analysis. Significant homology in this case is defined here as having an e-score of 1e⁻⁶⁰ or less with allowances made for human judgment based on the length and quality of the alignment. This step yielded 109 potential proteases for the list.

The ORFs were also analyzed by the protein signature family searching program InterProScan (Quevillon et. al. 2005) against the InterPro Database version 7.0 (Mulder et. al. 2005). The ORFs were assigned protein families by the InterProScan software as well as Gene Ontology (GO) categories associated with those families (Gene Ontology Consortium. 2004). Using these automatic GO assignments, all of the ORFs which had been assigned a GO name that contained the strings “peptidase”, “protease” or “proteolysis” were added to the list for further analysis. This step yielded an additional 70 potential proteases that had not been identified in the previous step.

More ORFs were added to the list based on their curated function from the previous annotation (Ramseier et. al. 2001) containing the keywords “peptidase” or “protease”. This step yielded 32 potential proteases that again had not been identified in the previous steps.

The list was then analyzed to remove ORFs which had a low probability of encoding proteases. Again, the intent of this study was to be very inclusive but many of the ORFs assigned to the list by these semi-automated methods could be easily identified as not coding for proteases based on limited criteria and human judgment. The two most common reasons for excluding genes were the weak evidence that a certain ORF is actually a protease, or that a particular gene showed greatest homology with another protein known to be protease homolog but not a protease itself. The final list of P. fluorescens proteases has 90 members and is shown in Table 2.

Example 3 In Silico Cellular Location Prediction of the Folding Modulator and Protease Proteins

One of the strengths of the Pfenex Expression Technology™ is its ability to control the cellular compartment to which a particular heterologous protein can be segregated. Thus, the cellular compartments where the identified host cell folding modulator and protease proteins are located were predicted. To make these predictions, two programs were chosen. PsortB 2.0 combines the results of 12 separate algorithms, which predict the subcellular location of a given peptide. The majority of the algorithms rely on detecting homology between the query protein and proteins of known subcellular localization. PsortB also includes algorithms such as HMMTOP and SignalP, which detect the presence of transmembrane folding domains or type I secretion signal sequences, respectively, using Hidden Markov Models (HMM). In addition to the PsortB results, SignalP HMM was used to predict the presence of type I secretion signal sequences. This was necessary because the output of PsortB can be vague when a signal sequence is detected but no other specific information indicating the subcellular location is given. In these cases, PsortB indicates that the subcellular localization of the protein is unknown, because it really could segregate to any one of the cytoplasmic membrane, periplasm, outer membrane or extracellular compartments. However, it is informative enough to know that the protein is probably not located in the cytoplasm to make it worth noting that in the table. Thus, Table 2 lists the results of the PsortB algorithm except in cases where that result was unknown. In these cases the result of SignalP HMM alone is given with “Signal Peptide” indicating that a signal peptide was detected and “Non Secretory” indicating that no signal peptide was detected.

Example 4 Construction of Plasmids that Enable the Co-Overexpression of Folding Modulators

Folding modulator genes were cloned into a plasmid derivative of pCN (Nieto et al. 1990), which is compatible with another plasmid that routinely is used to express the heterologous protein of interest (Squires et al. 2004; Chew et al. 2005). The construction of a mannitol-inducible grpE-dnaKJ-containing plasmid is exemplified. Other folding modulators either as a single gene or as multiple genes when organized in operons were cloned similarly as outlined below.

Employing genomic DNA isolated from P. fluorescens MB214 (DNeasy; Qiagen, Valencia, Calif.) as a template and primers RC199 (5-ATATACTAGTAGGAGGTAACTTATGGCTGACGAACAGACGCA-3′) (SEQ ID NO:1) and RC200 (5′-ATATTCTAGATTACAGGTCGCCGAAGAAGC-3′) (SEQ ID NO:2), the grpE-dnaKJ genes were amplified using PfuTurbo (Stratagene, La Jolla, Calif.) as per the manufacturer's recommendations. The resulting 4 kb PCR product was digested with SpeI and XbaI (restriction sites underlined in the primers above) and ligated into pDOW2236 which is a derivative of pDOW1306-6 (Schneider et al. 2005b) to create pDOW2240 containing the grpE-dnaKJ operon under control of the tac promoter. Plasmid pDOW2240 was then digested with SpeI and HindIII and the resulting grpE-dnaKJ-containing 4.0 kb DNA fragment was gel-purified using Qiaquick (Qiagen, Valencia, Calif.) and ligated into pDOW2247, which is a derivative of pCN carrying the P. fluorescens mannitol-regulated promoter (Schneider et al. 2005a), that was also digested with SpeI and HindIII. The resulting plasmid, pDOW3501, contained the grpE-dnaKJ operon under the control of the mannitol promoter. Plasmid pDOW3501 was then transformed into DC388 and other uracil-auxotrophic strains by selecting on M9 glucose plates supplemented with 250 ug/ml uracil.

Example 5 Construction of P. fluorescens Strains with Genomic Deletions of Protease Genes

Plasmids that enabled the creation of genomic deletions were constructed by amplification of 500-1000 bp DNA fragments both 5′ and 3′ of the gene to be deleted. The resulting 5′ PCR product typically ends with the translational initiation codon (ATG or GTG or TGT) of the gene to be deleted while the 3′ PCR product typically begins with the stop codon (TAA or TGA or TAG) of the gene to be deleted. These two PCR products were fused together through an additional amplification step then cloned into pDOW1261 (FIG. 1) (Chew et al. 2005) using SOE PCR (Horton et al. 1990).

Example 6 High-Through-Put Growth and Analysis of Heterologous Protein Expression in P. fluorescens Strains: Monoclonal Antibody

Plasmid pDOW2787 encodes the monoclonal antibody (mAb) gal2; the heavy chain is expressed with a Pbp secretion leader and under control of the tac promoter. The light chain is expressed with an OprF secretion leader and under control of the mannitol promoter. The plasmid was electroporated into competent cells of 63 strains carrying either a directed gene deletion or pDOW2247 carrying a folding modulator for co-expression, and five control strains containing a wild type strain. Cells were cultured in replicate deep-well blocks containing growth medium with glycerol by shaking at 300 rpm. Protein expression was induced at 24 hrs with 0.1 mM isopropyl β-D-thiogalactopyranoside (IPTG) and 1% mannitol. At 24 hrs post-induction, aliquots were lysed, antigen-binding of the antigen was measured to quantitate amounts of active antibody. The value was divided by OD₆₀₀ to measure cell specific activity. Strains Δprc1, ΔdegP2, ΔLa2, ΔclpP, and Δprc2, Δprc2, the grpEdnaKJ co-expression strain, Δtig, ΔclpX, and Δlon were all 2.4-fold or more higher than the control strains, which was statistically significant (p<0.5). Soluble cells fractions were prepared from Δprc1, ΔdegP2, ΔLa2 and the grpEdnaKJ co-expression strain and subjected to Western analysis (FIG. 2). A band with a size consistent with fully assembled antibody was detected in the four test strains, but not in the control.

Example 7 High Throughput Evaluation of Protein Expression in E. coli and P. fluorescens

Construction of C-Terminal his-Tag Expression Clones

Seven open reading frames (ORFs) were amplified for ligation into the NheI-XhoI sites of the periplasmic vector pDOW3718: Map2K3, ApoAI, hGH, gal2 scFV, gal13 scFv, EPO, and IL2. Primers were designed with a NheI restriction site on the 5′ primer and a XhoI restriction site on the 3′ primer. PCR reactions were performed using Platinum PCR Supermix (Invitrogen cat#1306-016) and PCR products digested with NheI and XhoI in NEBuffer 2 (New England Biolabs), incubating 37° C. overnight, then purified using Qiaquick Extraction kit (Qiagen). The digested products were then ligated to NheI-XhoI digested pDOW3718 using T4 DNA ligase (NEB). Ligation products were transformed into electrocompetent P. fluorescens DC454 and transformants were selected on LB agar supplemented with 250 μg/mL uracil and 30 μg/mL tetracycline.

The same seven ORFs were also amplified and prepared for ligation into the NcoI-XhoI sites of pET22b (Novagen) for expression in E. coli. Primers were designed with an NcoI restriction site on the 5′ primer, and XhoI restriction site (HindIII for MAP2K3 and SalI for ApoAI) on the 3′ primer. PCR reactions and restriction digestion were performed as described above with the exception that restriction enzymes NcoI, HindIII, SalI and XhoI were used as required. The digested products were ligated to NcoI-XhoI digested pET22b using T4 DNA ligase (NEB), and the ligation products were transformed into chemically competent E. coli Top 10 cells. Transformants were selected in LB agar ampicillin plates (Teknova). Plasmid DNA was prepared (Qiagen) and screened for insert by PCR using T7 promoter and T7 terminator primers. Positive clones were sequenced to confirm insert sequence. One confirmed cloned plasmid for each was subsequently transformed into BL21(DE3) (Invitrogen) for expression analysis.

High Throughput Expression Analysis

The P. fluorescens strains were grown using a high throughput expression protocol. Briefly, seed cultures, grown in LB medium supplemented with 250 ug/mL uracil and 15 mg/mL tetracycline, were used to inoculate 0.5 mL of defined minimal salts medium without yeast extract (Teknova 3H1130) supplemented with 250 ug/mL uracil and 15 mg/mL, tetracycline and 5% glycerol as the carbon source in a 2.0 mL deep 96-well microtiter plate. Following an initial growth phase at 30° C. (24 hours), expression via the Ptac promoter was induced with 0.3 mM isopropyl-β-D-1-thiogalactopyranoside (IPTG).

The E. coli strains were grown in a 2.0 mL deep 96-well plate using Overnight Express™ autoinduction medium (Novagen). Briefly, seed cultures grown in LB medium supplemented with 100 μg/mL ampicillin (LBAmp) were used to inoculate 0.5 mL of LBAmp+Overnight Express™ prepared according to the manufacturer's protocol. The cultures were allowed to grow for 24 hours.

Cultures were sampled at the time of induction (I0), and at 24 hours post induction (I24). Cell density was measured by optical density at 600 nm (OD₆₀₀), and 25 μL of whole broth was removed at 124 and stored at −20° C. for later processing. The remainder of the culture (˜400 μL) was transferred to Eppendorf tubes and centrifuged 20,000×g for 2 minutes. The cell free broth fractions were removed to a 96-well plate and stored at −20° C. as were the cell pellets.

SDS-PAGE and Western Analyses

Soluble and insoluble fractions from culture samples were generated using Easy Lyse™ (Epicentre Technologies cat#RP03750). The 250 μL whole broth sample was lysed by adding 175 mL of Easy Lyse™ buffer, incubating with gentle rocking at room temperature for 30 minutes. The lysate was centrifuged at 14,000 rpm for 20 minutes (4° C.) and the supernatant removed. The supernatant was saved as the soluble fraction. The pellet (insoluble fraction) was then resuspended in an equal volume of lysis buffer and resuspended by pipetting up and down. For selected clones, cell free broth samples were thawed and analyzed without dilution. Samples were mixed 1:1 with 2× Laemmli sample buffer containing β-mercaptoethanol (BioRad cat#161-0737) and boiled for 5 minutes prior to loading 204 on a Bio-Rad Criterion 4-12% Criterion XT gel (BioRad cat#345-0124) and electrophoresis in 1×MES buffer (cat.#161-0789). Gels were stained with Simply Blue Safe Stain (Invitrogen cat# LC6060) according to the manufacturer's protocol and imaged using the Alpha Innotech Imaging system.

Soluble and insoluble fractions prepared and separated by SDS-PAGE as described above were transferred to nitrocellulose (BioRad cat#162-0232) using 1× transfer buffer (Invitrogen cat# NP0006) prepared according to manufacturer's protocol, for 1.5-2 hours at 100 V. After transfer, the blot was washed briefly in 1×PBS and then blocked overnight in Blocker Casein in PBS (Pierce cat#37528) at 4° C. The diluent was poured off and more diluent was added containing a 1:5,000 dilution of anti-histidine-HRP antibody. The blots were incubated 2 hours at room temperature. The diluent/antibody solution was then poured off and the blots washed in 1×PBST (Sigma #P-3563) with vigorous shaking for 5 minutes. The PBST was changed and washing was repeated twice. For development, the blots were removed from the PBST solution and immersed in prepared solution using the Immunopure Metal Enhanced DAB Substrate Kit (Pierce cat#34065). The blots were incubated with gentle shaking for 10 minutes and then removed from the solution and allowed to dry on paper. The blots were imaged, and densitometry was performed using an Alpha Innotech FluorImager.

HTP Expression Analysis of E. coli and P. fluorescens Recombinant Strains

P. fluorescens and E. coli strains were grown in 0.5 mL cultures in a 96 well format to evaluate expression of a variety of human proteins as well as 2 single chain antibodies. Each protein was cloned into the P. fluorescens periplasmic expression vector pDOW3718, and the E. coli periplasmic expression vector pET22B in frame with a C-terminal 6× histidine tag. P. fluorescens cultures were grown in Dow's standard high throughput medium, and E. coli cultures were grown in the autoinduction medium Overnight Express™. Growth of P. fluorescens expression strains was observed to reach A₆₀₀ units of 20-25 at the time of induction and ˜25-45 post induction.

FIG. 3 shows growth curves for P. fluorescens (filled symbols) and E. coli (open symbols) expression clones. Elapsed fermentation time in hours is shown on the X-axis and optical density measured at 600 nm (A₆₀₀) is shown on the Y-axis. The arrow indicates time of induction of P. fluorescens cultures.

The E. coli constructs reached an A₆₀₀ of ˜5-10 units at the time of harvest, with the exception of 1 strain, which reached an A₆₀₀ of ˜25 units after 24 hours of growth in autoinduction medium (FIG. 3, open circle). SDS-PAGE and Western analyses (FIG. 4) showed expression of recombinant protein for P. fluorescens in all cases tested, and for E. coli in all but one case tested (Epo). Differences in expression levels and solubility between strains were readily detectable. P. fluorescens showed an advantage in solubility for MAP2K3, Gal2 and Gal13 scFvs (1), hGH and IL2. Moreover, an advantage in secretion leader processing in P. fluorescens was observed for ApoAI, Gal2 scFv, hGH and I12. In E. coli, the pelB leader appeared to be unprocessed from these proteins by SDS-PAGE and Western analyses.

Example 8 High-Through-Put Growth and Analysis of Heterologous Protein Expression in P. fluorescens Strains: Increasing Expression of Interferon Alpha 2a

Construction of Protein Expression Plasmids

Standard cloning methods are used in the construction of plasmids that overexpress Interferon alpha 2a. The fragment containing the coding sequences is subcloned into 16 different expression vectors. The expression vectors each contain a periplasmic secretion leader, as shown in Table 11.

TABLE 11 Expression vectors Expression Secretion Vector Leader pDOW5201 Pbp pDOW5206 DsbA pDOW5209 Azu pDOW5217 LAO pDOW5220 Ibp S31A pDOW5223 TolB pDOW5226 Trc pDOW5235 FlgI pDOW5238 CupC2 pDOW5241 CupB2 pDOW5244 CupA2 pDOW5247 nikA pDOW5256 PorE pDOW5259 pbpA20V pDOW5262 DsbC pDOW5265 Bce

For the subcloning, a plasmid containing the coding sequence for a heterologous protein to be overexpressed is digested with appropriate restriction enzymes. The expression vectors are digested with the same restriction enzymes. The insert and vector DNA is ligated overnight with T4 DNA ligase (New England Biolabs; M0202S), then electroporated into competent P. fluorescens DC454 cells. The transformants are plated on M9 glucose agar (Teknova) and screened for an insert by PCR. Positive clones are selected and sequence-confirmed on both strands. Each sequence-confirmed plasmid is transformed into selected P. fluorescens host strains in a 96-well format, to obtain an expression system comprising the host strain and an expression vector. Expression of the coding gene is driven by an appropriate promoter, e.g., Ptac.

Transformation into the P. fluorescens host strains DC485 and DC487 is performed as follows: twenty five microliters of competent cells are thawed and transferred into a 96-well electroporation plate (BTX ECM630 Electroporator), and 1 μl miniprep plasmid DNA is added to each well. Cells are electroporated and subsequently resuspended in 75 μl HTP media with trace minerals, transferred to 96-well deep well plate with 400 μl M9 salts 1% glucose medium, and incubated at 30° C. with shaking for 48 hours.

Growth and Expression in 96-Well Format

Expression of the recombinant protein is evaluated under standard induction conditions at the HTP 96-well plate scale. The expression systems, each containing one of each of the 16 expression constructs, are grown in triplicate and expression from the heterologous gene promoter is induced. A standard expression system, e.g., DC454 transformed with one of the heterologous protein expression vectors used, is included on the array. A null strain comprising DC432 null strain containing a vector without an expression insert is also included.

Ten microliters of seed culture is transferred into triplicate 96-well deep well plates, each well containing 500 μl of HTP-YE medium, and incubated as before for 24 hours. Isopropyl βD-1 thiogalactopyranoside (IPTG) is added to each well for a final concentration of 0.3 mM to induce recombinant protein expression, 1% mannitol is used to induce expression of genes (e.g., encoding folding modulators or proteases having potential chaperone activity) present on secondary expression vectors, and the temperature is reduced to 25° C. Twenty four hours after induction, cells are normalized to OD₆₀₀=20. Samples can be normalized in phosphate buffered saline, pH 7.4 to a final volume of 4000 μL, in cluster tubes, e.g., using the Biomek FX liquid-handling system (Beckman Coulter), and frozen at −80° C. for later processing.

Sample Preparation and SDS-CGE

Soluble and insoluble fractions are prepared from the cultures by sonication followed by centrifugation. Frozen, normalized culture broth (200-400 μL) is sonicated for 10 minutes. The lysates are centrifuged at 14,000 rpm for 20 minutes (4° C.) and the supernatants removed by pipet (soluble fraction). The pellets are then resuspended in 200 μL of phosphate buffered saline (PBS), pH 7.4. Insoluble samples are prepared for SDS capillary gel electrophoresis (CGE) (Caliper Life Sciences, Protein Express LabChip Kit, Part 760301), in the presence of dithiothreitol (DTT).

An overview of growth before induction and 24 hours after induction are analyzed by the statistical analysis software JMP. The mean OD₆₀₀ for each expression strain after an initial 24-hour growth period and following the 24 hour induction period are determined.

Soluble and insoluble fractions are analyzed by SDS-CGE to assess expression of the recombinant protein. Strains showing signal above background (e.g., expression from the DC432 null strain) corresponding to induced, soluble protein are noted. Soluble recombinant protein expression and insoluble protein expression are observed. Based on comparison of total and soluble protein yield to those in an indicator strain, expression systems representing a diversity of expression strategies are selected to evaluate at fermentation scale, and an optimal expression system is selected for overexpression of the Interferon alpha 2a.

Example 9 High-Through-Put Growth and Analysis of Heterologous Protein Expression in P. fluorescens Strains: Overexpression of a Protein in Table 9

Using a method similar to that described in Example 8, the coding sequence for a heterologous protein listed in Table 9 is cloned into a series of P. fluorescens expression vectors. The insert is confirmed by sequencing, and the vectors transformed into P. fluorescens host cell populations. The resulting expression strains are grown and protein expression is induced, in a 96-well format. The cultures are evaluated for heterologous protein yield. At least one optimal expression system is selected for overexpression based on the yields observed.

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Table of SEQ ID NOS: PROTEIN FOLDING MODULATOR PROTEASE (RXF #) SEQ ID NO: (RXF #) SEQ ID NO: LEADER/RELATED SEQUENCE SEQ ID NO: RXF02095.1 3 RXF00133.1 46 Pbp mutant leader - 159 DNA sequence RXF06767.1 4 RXF00285.2 47 Pbp mutant leader - 160 amino acid sequence RXF01748.1 5 RXF00325.1 48 DsbA leader - DNA 161 sequence RXF03385.1 6 RXF00428.1 49 DsbA leader - amino 162 acid sequence RXF05399.1 7 RXF00449.1 50 DsbC leader - DNA 163 sequence RXF06954.1 8 RXF00458.2 51 DsbC leader - amino 164 acid sequence RXF03376.1 9 RXF00561.2 52 Bce leader - DNA 165 sequence RXF03987.2 10 RXF00670.1 53 Bce leader - amino 166 acid sequence RXF05406.2 11 RXF00811.1 54 CupA2 leader - 167 DNA sequence RXF03346.2 12 RXF01037.1 55 CupA2 leader - 168 amino acid sequence RXF05413.1 13 RXF01181.1 56 CupB2 leader - DNA 169 sequence RXF04587.1 14 RXF01250.2 57 CupB2 leader - 170 amino acid sequence RXF08347.1 15 RXF01291.2 58 CupC2 leader - DNA 171 sequence RXF04654.2 16 RXF01418.1 59 CupC2 leader - 172 amino acid sequence RXF04663.1 17 RXF01590.2 60 NikA leader - DNA 173 sequence RXF01957.2 18 RXF01816.1 61 NikA leader - amino 174 acid sequence RXF01961.2 19 RXF01822.2 62 FlgI leader - DNA 175 sequence RXF04254.2 20 RXF01918.1 63 FlgI leader - amino 176 acid sequence RXF05455.2 21 RXF01919.1 64 ORF5550 leader - 177 DNA sequence RXF02231.1 22 RXF01961.2 65 ORF5550 leader - 178 amino acid sequence RXF07017.2 23 RXF01968.1 66 Ttg2C leader - DNA 179 sequence RXF08657.2 24 RXF02003.2 67 Ttg2C leader - 180 amino acid sequence RXF01002.1 25 RXF02151.2 68 Methyl - accepting 181 chemotaxis protein leader - DNA sequence RXF03307.1 26 RXF02161.1 69 Methyl - accepting 182 chemotaxis protein leader - amino acid sequence RXF04890.2 27 RXF02342.1 70 oligonucleotide 183 primer RXF03768.1 28 RXF02492.1 71 oligonucleotide 184 primer RXF05345.2 29 RXF02689.2 72 First 5 amino acids of the 185 predicted protein sequence for the processed form of dsbC-Skp RXF06034.2 30 RXF02739.1 73 First 10 amino acids of the 186 predicted protein sequence for the unprocessed form of DsbC-Skp RXF06591.1 31 RXF02796.1 74 First 10 amino acids of the 187 predicted protein sequence for the processed form of DsbC-Skp RXF05753.2 32 RXF02980.1 75 Porin E1 precursor 188 leader - DNA sequence RXF01833.2 33 RXF03065.2 76 Porin E1 precursor 189 leader - amino acid sequence RXF04655.2 34 RXF03329.2 77 Outer membrane porin F 190 leader - DNA sequence RXF05385.1 35 RXF03364.1 78 Outer membrane porin F 191 leader - amino acid sequence RXF00271.1 36 RXF03397.1 79 Periplasmic phosphate 192 binding protein (pbp) leader - DNA sequence RXF06068.1 37 RXF03441.1 80 Periplasmic phosphate 193 binding protein (pbp) leader - amino acid sequence RXF05719.1 38 RXF03488.2 81 Azurin leader - DNA 194 sequence RXF03406.2 39 RXF03699.2 82 Azurin leader - amino 195 acid sequence RXF04296.1 40 RXF03916.1 83 Lipoprote in B precursor 196 leader - DNA sequence RXF04553.1 41 RXF04047.2 84 Lipoprote in B precursor 197 leader - amino acid sequence RXF04554.2 42 RXF04052.2 85 Lysine-arginine-ornithine- 198 binding protein leader - DNA sequence RXF05310.2 43 RXF04304.1 86 Lysine-arginine-ornithine- 199 binding protein leader - amino acid sequence RXF05304.1 44 RXF04424.2 87 Iron(III) binding protein 200 leader - DNA sequence RXF05073.1 45 RXF04495.2 88 Iron(III) binding protein 201 leader - amino acid sequence RXF02090 137 RXF04500.1 89 N-terminal amino acid 202 sequence of processed azurin and ibp RXF01181.1 138 RXF04567.1 90 CDS-1 DNA sequence 203 RXF03364.1 139 RXF04631.2 91 CDS-1 amino acid 204 sequence RXF03376.1 140 RXF04653.2 92 TrxA DNA sequence 205 RXF04693.1 141 RXF04657.2 93 TrxA amino acid 206 sequences RXF05319.1 142 RXF04663.1 94 TolB leader - DNA 207 sequence RXF05445.1 143 RXF04692.1 95 TolB leader - amino 208 acid sequence RXF08122.2 144 RXF04693.1 96 Iron (III) binding protein 329 leader variant S31A - DNA sequence RXF06751.1 145 RXF04715.1 97 Iron (III) binding protein 330 leader variant S31A - amino acid sequence RXF00922.1 146 RXF04802.1 98 RXF03204.1 147 RXF04808.2 99 RXF04886.2 148 RXF04920.1 100 RXF05426.1 149 RXF04923.1 101 RXF05432.1 150 RXF04960.2 102 RXF04968.2 103 RXF04971.2 104 RXF05081.1 105 RXF05113.2 106 RXF05137.1 107 RXF05236.1 108 RXF05379.1 109 RXF05383.2 110 RXF05400.2 111 RXF05615.1 112 RXF05817.1 113 RXF05943.1 114 RXF06281.1 115 RXF06308.2 116 RXF06399.2 117 RXF06451.1 118 RXF06564.1 119 RXF06586.1 120 RXF06755.2 121 RXF06993.2 122 RXF07170.1 123 RXF07210.1 124 RXF07879.1 125 RXF08136.2 126 RXF08517.1 127 RXF08627.2 128 RXF08653.1 129 RXF08773.1 130 RXF08978.1 131 RXF09091.1 132 RXF09147.2 133 RXF09487.1 134 RXF09831.2 135 RXF04892.1 136 RXF00458.2 151 RXF01957.2 152 RXF04497.2 153 RXF04587.1 154 RXF04654.2 155 RXF04892.1 156 XFRNA203 157

All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims. 

That which is claimed:
 1. A method of assembling an array and using the array to simultaneously screen at least 10 nonidentical expression systems for testing expression of at least one heterologous recombinant protein, said method comprising: placing Pseudomonad or E. coli host cell populations in separate addressable locations of the array; introducing at least one expression vector encoding the at least one heterologous recombinant protein into each host cell population in the array to produce each of the at least 10 nonidentical expression systems in the array, wherein the array of at least 10 nonidentical expression systems includes at least 5 different host cell populations and at least 2 different expression vectors, wherein at least 3 of said at least 5 different host cell populations are deficient in their expression of at least one host cell protease, wherein the at least 10 nonidentical test expression systems in the array each comprises a different combination of a) a Pseudomonad or E. coli host cell population, and b) at least one of the at least 2 different expression vectors encoding the at least one heterologous recombinant protein, and simultaneously screening the at least 10 nonidentical test expression systems on the array; wherein at least one expression system in the array of the at least 10 nonidentical test expression systems overexpresses the at least one heterologous recombinant protein.
 2. The method of claim 1, wherein the at least 2 different expression vectors each encode a different heterologous recombinant protein.
 3. The method of claim 2, wherein the array includes at least 5 different expression vectors, and wherein each of said at least 5 different expression vectors encodes a different heterologous recombinant protein.
 4. The method of claim 1, wherein at least one expression vector encodes 2 different heterologous recombinant proteins.
 5. The method of claim 1, wherein at least 20 nonidentical test expression systems are placed in separate addressable locations, and wherein the array includes at least 10 different host cell populations and at least 2 different expression vectors, and further wherein at least 5 of said at least 10 different host cell populations are deficient in their expression of at least one host cell protease.
 6. The method of claim 1, wherein at least 50 nonidentical test expression systems are placed in separate addressable locations, and wherein the array includes at least 20 different host cell populations and at least 3 different expression vectors, and further wherein at least 10 of said at least 20 different host cell populations are deficient in their expression of at least one host cell protease.
 7. The method of claim 1 wherein the overexpression of the heterologous recombinant protein by the at least one expression system in the array of the at least 10 nonidentical test expression systems is an increase in yield of the heterologous recombinant protein, of about 1.5-fold to about 100-fold, relative to the yield in an indicator expression system.
 8. The method of claim 1 wherein the overexpression is a yield of the heterologous recombinant protein by the at least one expression system in the array of the at least 10 nonidentical test expression systems of about 10 mg/liter to about 2000 mg/liter.
 9. The method of claim 7 wherein the increase in yield is about 1.5-fold to about 100-fold.
 10. The method of claim 1 wherein the overexpression is a yield of the heterologous recombinant protein by the at least one expression system in the array of the at least 10 nonidentical test expression systems of about 0.1 mg/ml to about 50 mg/ml, wherein the heterologous recombinant protein is correctly processed protein.
 11. The method of claim 7 wherein the indicator expression system comprises a second expression system in the array of the at least 10 nonidentical test expression systems in the array, or a standard expression system.
 12. The method of claim 7, wherein the yield of the heterologous recombinant protein is a measure of the amount of soluble heterologous recombinant protein, the amount of recoverable heterologous recombinant protein, the amount of properly processed heterologous recombinant protein, the amount of properly folded heterologous recombinant protein, the amount of active heterologous recombinant protein, and/or the total amount of heterologous recombinant protein.
 13. The method of claim 7, further comprising selecting an optimal expression system from among the at least 10 nonidentical test expression systems based on the increased yield of the heterologous recombinant protein in the optimal expression system relative to that in the indicator expression system.
 14. The method of claim 8, further comprising selecting an optimal expression system from among the at least ten nonidentical test expression systems based on the yield of the heterologous recombinant protein in the optimal expression system.
 15. The method of claim 1, wherein at least 2 of said at least 5 different host cell populations overexpress at least one folding modulator.
 16. The method of claim 15, wherein the at least one folding modulator is encoded by a nucleic acid sequence selected from the group consisting of: SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, and SEQ ID NO:
 150. 17. The method of claim 15, wherein the at least one folding modulator is expressed from a plasmid.
 18. The method of claim 1, wherein at least one host cell population in the array is defective in at least one to about eight host cell proteases.
 19. The method of claim 18, wherein the at least one to about eight host cell proteases are selected from the proteases encoded by a nucleic acid sequence selected from the group consisting of: SEQ ID NO: 110, SEQ ID NO: 109, SEQ ID NO: 69, SEQ ID NO: 66, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 61, SEQ ID NO: 130, SEQ ID NO: 52, SEQ ID NO: 91, SEQ ID NO: 106, SEQ ID NO: 111, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 60, SEQ ID NO: 88, SEQ ID NO: 74, SEQ ID NO: 132, SEQ ID NO: 80, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 82, SEQ ID NO: 47, SEQ ID NO: 125, SEQ ID NO: 54, SEQ ID NO: 85, SEQ ID NO: 62, SEQ ID NO: 81, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 76, SEQ ID NO: 58, SEQ ID NO: 83, SEQ ID NO: 133, SEQ ID NO: 96, SEQ ID NO: 78, SEQ ID NO: 75, SEQ ID NO: 119, SEQ ID NO: 107, SEQ ID NO: 105, SEQ ID NO: 95, SEQ ID NO: 57, SEQ ID NO: 124, SEQ ID NO: 121, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 115, SEQ ID NO: 131, SEQ ID NO: 118, SEQ ID NO: 67, SEQ ID NO: 51, SEQ ID NO: 93, SEQ ID NO: 53, SEQ ID NO: 46, SEQ ID NO: 102, SEQ ID NO: 90, SEQ ID NO: 94, SEQ ID NO: 92, SEQ ID NO: 129, SEQ ID NO: 114, SEQ ID NO: 50, SEQ ID NO: 79, SEQ ID NO: 56, SEQ ID NO: 108, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 120, SEQ ID NO: 55, SEQ ID NO: 123, SEQ ID NO: 117, SEQ ID NO: 122, SEQ ID NO: 59, SEQ ID NO: 116, SEQ ID NO: 19, SEQ ID NO: 70, SEQ ID NO: 87, SEQ ID NO: 49, SEQ ID NO: 68, SEQ ID NO: 97, SEQ ID NO: 104, SEQ ID NO: 103, SEQ ID NO: 48, SEQ ID NO:72, SEQ ID NO: 73, SEQ ID NO: 77, SEQ ID NO: 71, SEQ ID NO: 84, SEQ ID NO: 126, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, and SEQ ID NO:
 157. 20. The method of claim 1, further comprising determining the number of cysteine residues in, the presence of clustered prolines in, the requirement of an N terminal methionine for activity of, or the presence of a small amino acid in the plus two position of, the heterologous recombinant protein.
 21. The method of claim 20, wherein when the heterologous recombinant protein has more than two cysteine residues, at least one of said at least 2 different expression systems overexpressing a folding modulator overexpresses a disulfide isomerase/oxidoreductase.
 22. The method of claim 21, wherein the disulfide isomerase/oxidoreductase is encoded on a plasmid.
 23. The method of claim 20, wherein when the heterologous recombinant protein has more than four cysteine residues, at least one of said at least 2 different expression vectors encoding the heterologous recombinant protein contains a periplasmic secretion leader coding sequence.
 24. The method of claim 20, wherein when the heterologous recombinant protein has more than four cysteine residues, at least one of said at least 2 different expression vectors encoding the heterologous recombinant protein contains a high or medium ribosome binding sequence.
 25. The method of claim 23, further wherein said at least one of said at least 2 different expression vectors encoding the heterologous recombinant protein and containing a periplasmic secretion leader coding sequence is included in at least one expression system that overexpresses at least one periplasmic chaperone, and at least one expression system that overexpresses at least one cytoplasmic chaperone.
 26. The method of claim 20, wherein when the heterologous protein has fewer than four cysteine residues, at least one of said at least 2 different expression vectors encoding the heterologous recombinant protein does not contain a periplasmic secretion leader coding sequence, and further wherein said at least one of said at least 2 different expression vectors encoding the heterologous recombinant protein and not containing a periplasmic secretion leader coding sequence is included in at least one expression system that overexpresses at least one cytoplasmic chaperone.
 27. The method of claim 20, wherein when clustered prolines are present, at least one expression system that overexpresses at least one 2+ peptidyl-prolyl cis-trans isomerase (PPIase) is included in the array.
 28. The method of claim 27, wherein the 2+ peptidyl-prolyl cis-trans isomerase (PPIase) is encoded on a plasmid.
 29. The method of claim 20, wherein when the N-terminal methionine is required, at least one expression system comprising a host cell population that has at least one defect in at least one host cell methionyl amino peptidase, is included in the array.
 30. The method of claim 20 wherein when a small amino acid is present in the plus two position of the heterologous recombinant protein, at least one expression system comprising a host cell population that has at least one defect in at least one amino peptidase, is included in the array.
 31. The method of claim 20, wherein the small amino acid is selected from the group consisting of: glycine, alanine, valine, serine, threonine, aspartic acid, asparagine, and proline.
 32. The method of claim 1, wherein the heterologous recombinant protein is selected from the group consisting of: a toxin; a cytokine, growth factor or hormone, or receptor thereof; an antibody or antibody derivative; a human therapeutic protein or therapeutic enzyme; a non-natural protein or a fusion protein; a chaperone; a pathogen protein or pathogen-derived antigen; a lipoprotein; a reagent protein; and a biocatalytic enzyme.
 33. The method of claim 32, wherein the toxin is a vertebrate or invertebrate animal toxin, a plant toxin, a bacterial toxin, a fungal toxin, or variant thereof.
 34. The method of claim 32, wherein the antibody or antibody derivative is a humanized antibody, modified antibody, nanobody, bispecific antibody, single-chain antibody, Fab, Domain antibody, shark single domain antibody, camelid single domain antibody, linear antibody, diabody, or BiTE molecule.
 35. The method of claim 1, wherein at least 10% of the heterologous recombinant protein is insoluble when expressed in an indicator strain, or wherein the heterologous recombinant protein is predicted to be insoluble using a protein solubility prediction tool.
 36. The method of claim 8, wherein the yield of the heterologous recombinant protein is a measure of the amount of soluble heterologous recombinant protein, the amount of recoverable heterologous recombinant protein, the amount of properly processed heterologous recombinant protein, the amount of properly folded heterologous recombinant protein, the amount of active heterologous recombinant protein, and/or the total amount of heterologous recombinant protein.
 37. The method of claim 1, wherein at least one of said at least 2 different expression vectors encodes a periplasmic secretion leader sequence operably linked to the heterologous recombinant protein.
 38. The method of claim 1, wherein the overexpression is a yield of the heterologous recombinant protein of about 10 mg/ml to about 25 mg/ml in the periplasmic compartment of the host cell of the at least one nonidentical test expression system. 